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Iron in PDB 8qjg: Crystal Structure of Cytochrome Domain 2 From Pgca

Protein crystallography data

The structure of Crystal Structure of Cytochrome Domain 2 From Pgca, PDB code: 8qjg was solved by B.W.Nash, M.J.Edwards, T.A.Clarke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.96 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 95.104, 74.101, 56.019, 90, 103.92, 90
R / Rfree (%) 17.5 / 22.7

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Cytochrome Domain 2 From Pgca (pdb code 8qjg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of Cytochrome Domain 2 From Pgca, PDB code: 8qjg:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 8qjg

Go back to Iron Binding Sites List in 8qjg
Iron binding site 1 out of 6 in the Crystal Structure of Cytochrome Domain 2 From Pgca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Cytochrome Domain 2 From Pgca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe103

b:8.1
occ:1.00
FE A:HEC103 0.0 8.1 1.0
NB A:HEC103 2.0 5.4 1.0
NA A:HEC103 2.0 9.5 1.0
NC A:HEC103 2.0 15.0 1.0
ND A:HEC103 2.1 2.3 1.0
NE2 A:HIS17 2.1 5.7 1.0
SD A:MET44 2.4 8.4 1.0
CD2 A:HIS17 2.9 9.2 1.0
C4B A:HEC103 3.0 7.8 1.0
C1B A:HEC103 3.0 7.7 1.0
C1C A:HEC103 3.0 10.4 1.0
C1A A:HEC103 3.0 12.3 1.0
C1D A:HEC103 3.1 3.9 1.0
C4D A:HEC103 3.1 9.1 1.0
C4A A:HEC103 3.1 6.7 1.0
C4C A:HEC103 3.1 11.7 1.0
CE1 A:HIS17 3.2 7.7 1.0
CHC A:HEC103 3.3 10.0 1.0
CHA A:HEC103 3.4 8.2 1.0
CG A:MET44 3.4 7.2 1.0
CHB A:HEC103 3.4 3.6 1.0
CHD A:HEC103 3.5 11.0 1.0
CE A:MET44 3.6 9.1 1.0
CG A:HIS17 4.2 6.6 1.0
C3B A:HEC103 4.2 12.2 1.0
C2B A:HEC103 4.2 12.1 1.0
ND1 A:HIS17 4.2 6.3 1.0
C2C A:HEC103 4.2 10.2 1.0
C2A A:HEC103 4.3 6.1 1.0
C2D A:HEC103 4.3 9.0 1.0
C3C A:HEC103 4.3 9.2 1.0
C3D A:HEC103 4.3 9.9 1.0
C3A A:HEC103 4.3 5.1 1.0
CB A:MET44 4.8 6.4 1.0
O A:ARG41 4.9 6.1 1.0

Iron binding site 2 out of 6 in 8qjg

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Iron binding site 2 out of 6 in the Crystal Structure of Cytochrome Domain 2 From Pgca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Cytochrome Domain 2 From Pgca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe102

b:7.9
occ:1.00
FE B:HEC102 0.0 7.9 1.0
NC B:HEC102 2.0 8.9 1.0
NE2 B:HIS17 2.0 9.5 1.0
NA B:HEC102 2.0 10.1 1.0
NB B:HEC102 2.1 5.2 1.0
ND B:HEC102 2.1 4.7 1.0
SD B:MET44 2.5 6.6 1.0
CD2 B:HIS17 3.0 6.9 1.0
C1C B:HEC102 3.0 8.8 1.0
C4B B:HEC102 3.0 9.0 1.0
C1A B:HEC102 3.0 10.5 1.0
CE1 B:HIS17 3.0 9.3 1.0
C1D B:HEC102 3.0 4.2 1.0
C4C B:HEC102 3.1 11.6 1.0
C4D B:HEC102 3.1 8.4 1.0
C1B B:HEC102 3.1 6.2 1.0
C4A B:HEC102 3.1 5.5 1.0
CE B:MET44 3.2 11.3 1.0
CHC B:HEC102 3.4 10.7 1.0
CHA B:HEC102 3.4 11.4 1.0
CHD B:HEC102 3.4 8.4 1.0
CHB B:HEC102 3.5 5.0 1.0
CG B:MET44 3.5 9.1 1.0
ND1 B:HIS17 4.1 10.8 1.0
CG B:HIS17 4.1 11.9 1.0
C2C B:HEC102 4.2 10.5 1.0
C3B B:HEC102 4.3 9.5 1.0
C2B B:HEC102 4.3 13.8 1.0
C3C B:HEC102 4.3 10.0 1.0
C2A B:HEC102 4.3 6.0 1.0
C2D B:HEC102 4.3 5.7 1.0
C3A B:HEC102 4.3 4.0 1.0
C3D B:HEC102 4.3 7.0 1.0
CB B:MET44 4.9 9.2 1.0
O B:ARG41 5.0 8.7 1.0

Iron binding site 3 out of 6 in 8qjg

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Iron binding site 3 out of 6 in the Crystal Structure of Cytochrome Domain 2 From Pgca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Cytochrome Domain 2 From Pgca within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe104

b:9.3
occ:1.00
FE C:HEC104 0.0 9.3 1.0
NE2 C:HIS17 2.0 10.0 1.0
NC C:HEC104 2.0 8.0 1.0
NB C:HEC104 2.0 10.3 1.0
ND C:HEC104 2.0 4.9 1.0
NA C:HEC104 2.1 12.1 1.0
SD C:MET44 2.4 8.6 1.0
CE1 C:HIS17 3.0 7.7 1.0
C4C C:HEC104 3.0 8.3 1.0
CD2 C:HIS17 3.0 9.5 1.0
C4B C:HEC104 3.0 9.5 1.0
C1D C:HEC104 3.0 8.9 1.0
C1B C:HEC104 3.0 13.2 1.0
C4D C:HEC104 3.1 5.8 1.0
C4A C:HEC104 3.1 8.4 1.0
C1C C:HEC104 3.1 9.7 1.0
C1A C:HEC104 3.1 11.9 1.0
CHD C:HEC104 3.4 10.5 1.0
CG C:MET44 3.4 6.4 1.0
CHB C:HEC104 3.4 8.0 1.0
CHC C:HEC104 3.4 14.1 1.0
CHA C:HEC104 3.4 10.4 1.0
CE C:MET44 3.5 7.9 1.0
ND1 C:HIS17 4.1 9.7 1.0
CG C:HIS17 4.1 10.1 1.0
C3B C:HEC104 4.2 11.1 1.0
C2B C:HEC104 4.2 12.1 1.0
C3C C:HEC104 4.3 10.4 1.0
C2D C:HEC104 4.3 6.8 1.0
C2C C:HEC104 4.3 10.2 1.0
C3D C:HEC104 4.3 5.6 1.0
C3A C:HEC104 4.3 9.2 1.0
C2A C:HEC104 4.3 9.1 1.0
CB C:MET44 4.8 7.0 1.0
O C:ARG41 4.9 8.0 1.0

Iron binding site 4 out of 6 in 8qjg

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Iron binding site 4 out of 6 in the Crystal Structure of Cytochrome Domain 2 From Pgca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Cytochrome Domain 2 From Pgca within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe104

b:9.1
occ:1.00
FE D:HEC104 0.0 9.1 1.0
NE2 D:HIS17 2.0 9.1 1.0
NB D:HEC104 2.0 6.2 1.0
NA D:HEC104 2.0 12.1 1.0
NC D:HEC104 2.1 16.2 1.0
ND D:HEC104 2.1 7.6 1.0
SD D:MET44 2.5 9.1 1.0
CD2 D:HIS17 3.0 10.7 1.0
CE1 D:HIS17 3.0 6.9 1.0
C1B D:HEC104 3.0 8.5 1.0
C4B D:HEC104 3.0 7.8 1.0
C1C D:HEC104 3.0 9.7 1.0
C1A D:HEC104 3.1 7.4 1.0
C4A D:HEC104 3.1 8.8 1.0
C1D D:HEC104 3.1 6.2 1.0
C4D D:HEC104 3.1 11.2 1.0
C4C D:HEC104 3.1 12.7 1.0
CE D:MET44 3.2 10.3 1.0
CG D:MET44 3.4 7.8 1.0
CHC D:HEC104 3.4 6.2 1.0
CHB D:HEC104 3.4 5.5 1.0
CHA D:HEC104 3.4 10.3 1.0
CHD D:HEC104 3.5 10.2 1.0
ND1 D:HIS17 4.1 9.7 1.0
CG D:HIS17 4.1 11.5 1.0
C2B D:HEC104 4.2 7.5 1.0
C3B D:HEC104 4.2 8.5 1.0
C2C D:HEC104 4.3 11.2 1.0
C3A D:HEC104 4.3 6.6 1.0
C2A D:HEC104 4.3 7.0 1.0
C3C D:HEC104 4.3 8.7 1.0
C3D D:HEC104 4.3 8.3 1.0
C2D D:HEC104 4.4 5.7 1.0
CB D:MET44 4.8 8.9 1.0
O D:ARG41 4.9 8.4 1.0

Iron binding site 5 out of 6 in 8qjg

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Iron binding site 5 out of 6 in the Crystal Structure of Cytochrome Domain 2 From Pgca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Cytochrome Domain 2 From Pgca within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe103

b:9.3
occ:1.00
FE E:HEC103 0.0 9.3 1.0
NB E:HEC103 2.0 9.5 1.0
NE2 E:HIS17 2.0 9.3 1.0
NC E:HEC103 2.1 8.6 1.0
ND E:HEC103 2.1 5.6 1.0
NA E:HEC103 2.1 11.0 1.0
SD E:MET44 2.4 7.4 1.0
CE1 E:HIS17 3.0 7.8 1.0
C4B E:HEC103 3.0 7.7 1.0
C1B E:HEC103 3.0 18.5 1.0
CD2 E:HIS17 3.0 12.2 1.0
C1D E:HEC103 3.1 11.3 1.0
C4A E:HEC103 3.1 10.7 1.0
C1C E:HEC103 3.1 10.7 1.0
C4D E:HEC103 3.1 5.8 1.0
C4C E:HEC103 3.1 9.1 1.0
C1A E:HEC103 3.2 10.4 1.0
CG E:MET44 3.4 6.8 1.0
CHC E:HEC103 3.4 12.2 1.0
CHB E:HEC103 3.4 13.7 1.0
CHD E:HEC103 3.4 9.4 1.0
CE E:MET44 3.5 6.1 1.0
CHA E:HEC103 3.5 5.8 1.0
ND1 E:HIS17 4.1 9.7 1.0
CG E:HIS17 4.2 8.8 1.0
C2B E:HEC103 4.2 11.8 1.0
C3B E:HEC103 4.2 9.7 1.0
C2C E:HEC103 4.3 7.2 1.0
C2D E:HEC103 4.3 5.1 1.0
C3D E:HEC103 4.3 9.5 1.0
C3A E:HEC103 4.3 12.1 1.0
C3C E:HEC103 4.3 7.3 1.0
C2A E:HEC103 4.4 8.6 1.0
CB E:MET44 4.8 6.5 1.0
O E:ARG41 4.9 7.8 1.0

Iron binding site 6 out of 6 in 8qjg

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Iron binding site 6 out of 6 in the Crystal Structure of Cytochrome Domain 2 From Pgca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Cytochrome Domain 2 From Pgca within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe104

b:9.0
occ:1.00
FE F:HEC104 0.0 9.0 1.0
NB F:HEC104 2.0 9.6 1.0
NE2 F:HIS17 2.0 7.4 1.0
ND F:HEC104 2.0 9.7 1.0
NC F:HEC104 2.1 9.7 1.0
NA F:HEC104 2.1 10.1 1.0
SD F:MET44 2.4 8.4 1.0
CE1 F:HIS17 2.9 6.5 1.0
C1B F:HEC104 3.0 13.2 1.0
C4B F:HEC104 3.0 5.4 1.0
C1D F:HEC104 3.0 10.3 1.0
C4D F:HEC104 3.1 8.9 1.0
CD2 F:HIS17 3.1 9.1 1.0
C4A F:HEC104 3.1 5.3 1.0
C4C F:HEC104 3.1 7.5 1.0
C1C F:HEC104 3.1 7.1 1.0
C1A F:HEC104 3.1 8.3 1.0
CE F:MET44 3.4 4.6 1.0
CHD F:HEC104 3.4 7.9 1.0
CHB F:HEC104 3.4 10.3 1.0
CG F:MET44 3.4 8.8 1.0
CHC F:HEC104 3.5 9.9 1.0
CHA F:HEC104 3.5 4.6 1.0
ND1 F:HIS17 4.0 8.2 1.0
CG F:HIS17 4.2 7.7 1.0
C2B F:HEC104 4.2 12.4 1.0
C3B F:HEC104 4.2 12.0 1.0
C2D F:HEC104 4.3 8.9 1.0
C3D F:HEC104 4.3 10.8 1.0
C3A F:HEC104 4.3 8.4 1.0
C3C F:HEC104 4.3 5.6 1.0
C2C F:HEC104 4.3 10.0 1.0
C2A F:HEC104 4.3 8.0 1.0
CB F:MET44 4.8 9.8 1.0
O F:ARG41 4.9 8.6 1.0

Reference:

B.W.Nash, T.M.Fernandes, J.A.J.Burton, L.Morgado, J.H.Van Wonderen, D.A.Svistunenko, M.J.Edwards, C.A.Salgueiro, J.N.Butt, T.A.Clarke. Tethered Heme Domains in A Triheme Cytochrome Allow For Increased Electron Transport Distances. Protein Sci. V. 33 E5200 2024.
ISSN: ESSN 1469-896X
PubMed: 39470321
DOI: 10.1002/PRO.5200
Page generated: Wed Nov 13 09:48:24 2024

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