Bromine in PDB 4tpu: Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans

The structure of Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans, PDB code: 4tpu was solved by A.K.Kumar, H.P.Yennawar, N.H.Yennawar, J.G.Ferry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.47 / 2.36
Space group	P 2 3
Cell size a, b, c (Å), α, β, γ (°)	93.181, 93.181, 93.181, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 26.9

The structure of Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans also contains other interesting chemical elements:

Iron	(Fe)	5 atoms
Sodium	(Na)	4 atoms

The binding sites of Bromine atom in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans (pdb code 4tpu). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 7 binding sites of Bromine where determined in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans, PDB code: 4tpu:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7;

Bromine binding site 1 out of 7 in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Br307 b:85.8 occ:0.50 H A:ASP90 2.5 67.0 1.0 HA A:SER89 3.1 56.4 1.0 HB2 A:ASP90 3.1 67.0 1.0 N A:ASP90 3.3 56.0 1.0 HD13 A:LEU76 3.5 42.1 1.0 NA A:NA308 3.5 55.7 1.0 O A:HOH431 3.6 51.4 1.0 O A:HOH423 3.7 52.5 1.0 CB A:ASP90 3.8 55.9 1.0 HB3 A:ASP90 3.9 67.0 1.0 CA A:SER89 3.9 47.1 1.0 HB2 A:SER89 3.9 65.4 1.0 HD2 A:HIS23 3.9 55.4 1.0 HA A:TYR22 4.0 48.8 1.0 C A:SER89 4.0 55.4 1.0 CA A:ASP90 4.1 66.6 1.0 HD1 A:TYR22 4.2 43.5 1.0 HB3 A:LEU76 4.2 43.7 1.0 O A:GLY21 4.2 67.7 1.0 O A:HOH414 4.4 45.2 1.0 CB A:SER89 4.4 54.5 1.0 HA A:ASP90 4.4 79.8 1.0 CD1 A:LEU76 4.5 35.2 1.0 HD22 A:LEU76 4.5 42.1 1.0 HB3 A:SER89 4.6 65.4 1.0 CD1 A:TYR22 4.6 36.4 1.0 O A:VAL88 4.6 49.9 1.0 CD2 A:HIS23 4.7 46.2 1.0 HD12 A:LEU76 4.8 42.1 1.0 HE1 A:TYR22 4.9 44.0 1.0 HD11 A:LEU76 4.9 42.1 1.0 CA A:TYR22 5.0 40.7 1.0 HE2 A:HIS23 5.0 74.9 1.0

Bromine binding site 2 out of 7 in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Br310 b:81.3 occ:1.00 HA A:PRO74 2.9 45.4 1.0 NA A:NA309 3.4 47.6 1.0 HD22 A:ASN77 3.5 85.3 1.0 HG3 A:PRO74 3.7 56.3 1.0 CA A:PRO74 3.7 37.9 1.0 HB3 A:PRO74 3.9 45.7 1.0 N A:PRO74 4.0 44.1 1.0 HB3 A:ASN77 4.1 56.0 1.0 HB3 A:ASP73 4.2 52.5 1.0 ND2 A:ASN77 4.2 71.1 1.0 CB A:PRO74 4.2 38.2 1.0 CG A:PRO74 4.3 47.0 1.0 HB2 A:ASN77 4.3 56.0 1.0 C A:ASP73 4.4 37.3 1.0 O A:ASP73 4.4 43.8 1.0 HD3 A:PRO74 4.6 59.7 1.0 CB A:ASN77 4.6 46.8 1.0 CD A:PRO74 4.6 49.8 1.0 HD21 A:ASN77 4.6 85.3 1.0 CG A:ASN77 4.8 56.4 1.0 CB A:ASP73 5.0 43.8 1.0

Bromine binding site 3 out of 7 in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Br311 b:68.1 occ:0.50 HB2 A:TYR47 2.9 56.8 1.0 H A:TRP48 3.1 59.1 1.0 HA A:TYR47 3.1 62.5 1.0 HG21 A:ILE66 3.2 52.0 1.0 HD13 A:ILE66 3.3 43.1 1.0 NA A:NA315 3.3 55.8 1.0 HE3 A:LYS59 3.4 79.6 1.0 HB3 A:TYR47 3.4 56.8 1.0 CB A:TYR47 3.5 47.4 1.0 HG23 A:ILE66 3.6 52.0 1.0 CA A:TYR47 3.8 52.1 1.0 HE2 A:LYS59 3.8 79.6 1.0 N A:TRP48 3.9 49.4 1.0 CG2 A:ILE66 3.9 43.4 1.0 CE A:LYS59 4.0 66.4 1.0 HZ1 A:LYS59 4.0 94.3 1.0 CD1 A:ILE66 4.2 36.0 1.0 HB2 A:TRP48 4.3 69.9 1.0 C A:TYR47 4.3 53.1 1.0 HG22 A:ILE66 4.4 52.0 1.0 NZ A:LYS59 4.5 78.7 1.0 HD11 A:ILE66 4.6 43.1 1.0 HG12 A:ILE66 4.6 66.2 1.0 HD12 A:ILE66 4.8 43.1 1.0 HG3 A:LYS59 4.8 75.8 1.0 O A:GLY46 4.8 61.7 1.0 CG1 A:ILE66 4.9 55.2 1.0 CG A:TYR47 4.9 55.3 1.0 OE1 A:GLU42 4.9 86.5 1.0 HZ2 A:LYS59 4.9 94.3 1.0 CB A:ILE66 5.0 45.6 1.0

Bromine binding site 4 out of 7 in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Br312 b:73.2 occ:0.50 H A:ARG170 2.4 42.5 1.0 O A:HOH422 2.8 48.1 1.0 HA A:GLU169 3.0 43.4 1.0 N A:ARG170 3.2 35.5 1.0 HG3 A:ARG170 3.3 60.4 1.0 HB2 A:GLU169 3.4 48.0 1.0 HB2 A:ARG170 3.5 47.2 1.0 HZ3 A:TRP140 3.5 59.4 1.0 CA A:GLU169 3.7 36.2 1.0 C A:GLU169 4.0 39.7 1.0 CB A:GLU169 4.0 40.0 1.0 CG A:ARG170 4.0 50.4 1.0 CB A:ARG170 4.1 39.4 1.0 HD2 A:ARG170 4.2 66.7 1.0 CA A:ARG170 4.2 38.1 1.0 HB3 A:GLU169 4.3 48.0 1.0 CZ3 A:TRP140 4.4 49.5 1.0 HD3 A:ARG170 4.4 66.7 1.0 CD A:ARG170 4.5 55.7 1.0 HH2 A:TRP140 4.7 57.8 1.0 HG2 A:ARG170 4.8 60.4 1.0 O A:ARG170 4.9 38.4 1.0 O A:PHE168 4.9 44.7 1.0 HA A:ARG170 4.9 45.6 1.0 CH2 A:TRP140 5.0 48.2 1.0 HB3 A:ARG170 5.0 47.2 1.0

Bromine binding site 5 out of 7 in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Br313 b:87.5 occ:0.50 HB A:ILE102 2.6 73.5 1.0 O A:ILE102 2.7 48.6 1.0 O A:TYR83 2.9 47.4 1.0 H A:ILE102 3.0 85.7 1.0 O A:HOH441 3.0 60.6 1.0 HD1 A:TYR83 3.2 53.3 1.0 HD12 A:ILE102 3.3 70.6 1.0 HE1 A:TYR83 3.4 60.9 1.0 CD1 A:TYR83 3.4 44.5 1.0 CB A:ILE102 3.5 61.3 1.0 HD13 A:ILE102 3.5 70.6 1.0 CE1 A:TYR83 3.5 50.8 1.0 C A:ILE102 3.6 56.1 1.0 HA A:TYR83 3.6 48.5 1.0 N A:ILE102 3.7 71.5 1.0 CA A:ILE102 3.8 71.2 1.0 CD1 A:ILE102 3.8 58.9 1.0 C A:TYR83 3.9 44.2 1.0 N1 A:URE305 4.0 79.7 1.0 HN11 A:URE305 4.0 95.6 1.0 C A:URE305 4.0 83.8 1.0 O A:URE305 4.1 79.7 1.0 CG1 A:ILE102 4.2 57.4 1.0 CG A:TYR83 4.3 40.2 1.0 CA A:TYR83 4.3 40.5 1.0 HN12 A:URE305 4.4 95.6 1.0 HG22 A:ILE102 4.4 70.2 1.0 CZ A:TYR83 4.5 52.8 1.0 CG2 A:ILE102 4.5 58.6 1.0 N2 A:URE305 4.7 69.3 1.0 HD11 A:ILE102 4.7 70.6 1.0 HG21 A:ILE102 4.7 70.2 1.0 HA A:ILE102 4.7 85.3 1.0 HA A:SER101 4.8 0.5 1.0 HG13 A:ILE102 4.8 68.8 1.0 CB A:TYR83 4.9 36.8 1.0 N A:PRO103 4.9 50.5 1.0 HG12 A:ILE102 4.9 68.8 1.0 C A:SER101 4.9 93.5 1.0

Bromine binding site 6 out of 7 in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Br314 b:79.7 occ:0.50 OE2 A:GLU91 4.7 98.4 1.0

Bromine binding site 7 out of 7 in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Br316 b:0.0 occ:0.50 HH12 A:ARG43 4.5 0.0 1.0 NH1 A:ARG43 4.5 0.8 1.0 CZ A:ARG43 4.6 95.7 1.0 HH22 A:ARG43 4.8 0.7 1.0 NH2 A:ARG43 4.8 99.0 1.0 HH11 A:ARG43 4.8 0.0 1.0

A.K.Kumar, R.S.Kumar, N.H.Yennawar, H.P.Yennawar, J.G.Ferry. Structural and Biochemical Characterization of A Ferredoxin:Thioredoxin Reductase-Like Enzyme From Methanosarcina Acetivorans. Biochemistry 2015.
ISSN: ISSN 0006-2960
PubMed: 25915695
DOI: 10.1021/ACS.BIOCHEM.5B00137