Atomistry » Iron » PDB 5exd-5foi » 5fle
Atomistry »
  Iron »
    PDB 5exd-5foi »
      5fle »

Iron in PDB 5fle: High Resolution Ni,Fe-Codh-320 Mv with Cn State

Protein crystallography data

The structure of High Resolution Ni,Fe-Codh-320 Mv with Cn State, PDB code: 5fle was solved by A.Ciaccafava, D.Tombolelli, L.Domnik, J.Fesseler, J.-H.Jeoung, H.Dobbek, M.A.Mroginski, P.Hildebrandt, I.Zebger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.17 / 1.23
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.216, 75.511, 71.132, 90.00, 111.53, 90.00
R / Rfree (%) 12.1 / 15.3

Other elements in 5fle:

The structure of High Resolution Ni,Fe-Codh-320 Mv with Cn State also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the High Resolution Ni,Fe-Codh-320 Mv with Cn State (pdb code 5fle). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the High Resolution Ni,Fe-Codh-320 Mv with Cn State, PDB code: 5fle:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 5fle

Go back to Iron Binding Sites List in 5fle
Iron binding site 1 out of 10 in the High Resolution Ni,Fe-Codh-320 Mv with Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of High Resolution Ni,Fe-Codh-320 Mv with Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1001

b:8.2
occ:1.00
 FE1 X:SF41001 0.0 8.2 1.0
S3 X:SF41001 2.3 8.1 1.0
SG X:CYS70 2.3 8.3 1.0
S4 X:SF41001 2.3 8.1 1.0
S2 X:SF41001 2.3 8.4 1.0
FE2 X:SF41001 2.7 8.0 1.0
FE4 X:SF41001 2.7 8.2 1.0
FE3 X:SF41001 2.8 8.1 1.0
CB X:CYS70 3.4 8.2 1.0
N X:CYS70 3.8 8.4 1.0
S1 X:SF41001 3.9 8.0 1.0
O X:HOH2184 4.2 8.6 1.0
NH2 X:ARG80 4.2 9.2 1.0
CA X:CYS70 4.2 8.6 1.0
CB X:ALA72 4.4 9.9 1.0
CG X:MET199 4.6 7.7 1.0
N X:ILE69 4.7 7.3 1.0
SG X:CYS51 4.7 8.7 1.0
SG X:CYS48 4.8 8.1 1.0
SG X:CYS56 4.8 8.6 1.0
C X:ILE69 5.0 8.4 1.0

Iron binding site 2 out of 10 in 5fle

Go back to Iron Binding Sites List in 5fle
Iron binding site 2 out of 10 in the High Resolution Ni,Fe-Codh-320 Mv with Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of High Resolution Ni,Fe-Codh-320 Mv with Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1001

b:8.0
occ:1.00
 FE2 X:SF41001 0.0 8.0 1.0
S4 X:SF41001 2.2 8.1 1.0
S1 X:SF41001 2.3 8.0 1.0
SG X:CYS48 2.3 8.1 1.0
S3 X:SF41001 2.3 8.1 1.0
FE4 X:SF41001 2.7 8.2 1.0
FE3 X:SF41001 2.7 8.1 1.0
FE1 X:SF41001 2.7 8.2 1.0
CB X:CYS48 3.2 7.7 1.0
NH2 X:ARG80 3.7 9.2 1.0
S2 X:SF41001 3.8 8.4 1.0
N X:HIS50 4.0 7.2 1.0
C X:CYS48 4.2 7.6 1.0
O X:CYS48 4.2 8.1 1.0
CA X:CYS48 4.3 7.0 1.0
CB X:HIS50 4.3 8.3 1.0
N X:CYS51 4.5 7.9 1.0
CA X:HIS50 4.5 7.6 1.0
N X:ARG49 4.6 7.5 1.0
SG X:CYS56 4.7 8.6 1.0
CB X:CYS56 4.7 8.3 1.0
C X:HIS50 4.7 8.0 1.0
CZ X:ARG80 4.8 8.0 1.0
SG X:CYS70 4.9 8.3 1.0
SG X:CYS51 4.9 8.7 1.0
C X:ARG49 4.9 8.0 1.0

Iron binding site 3 out of 10 in 5fle

Go back to Iron Binding Sites List in 5fle
Iron binding site 3 out of 10 in the High Resolution Ni,Fe-Codh-320 Mv with Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of High Resolution Ni,Fe-Codh-320 Mv with Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1001

b:8.1
occ:1.00
 FE3 X:SF41001 0.0 8.1 1.0
S1 X:SF41001 2.2 8.0 1.0
SG X:CYS51 2.3 8.7 1.0
S2 X:SF41001 2.3 8.4 1.0
S4 X:SF41001 2.3 8.1 1.0
FE2 X:SF41001 2.7 8.0 1.0
FE4 X:SF41001 2.7 8.2 1.0
FE1 X:SF41001 2.8 8.2 1.0
CB X:CYS51 3.3 8.0 1.0
N X:CYS51 3.5 7.9 1.0
CA X:CYS51 3.8 7.9 1.0
S3 X:SF41001 3.9 8.1 1.0
O X:CYS51 4.2 8.6 1.0
C X:CYS51 4.2 7.3 1.0
C X:HIS50 4.3 8.0 1.0
CG X:MET199 4.4 7.7 1.0
N X:GLY54 4.4 9.0 1.0
CB X:GLN53 4.6 8.7 1.0
N X:HIS50 4.8 7.2 1.0
SG X:CYS48 4.8 8.1 1.0
CB X:MET199 4.8 7.5 1.0
SG X:CYS56 4.8 8.6 1.0
SG X:CYS70 4.8 8.3 1.0
N X:GLN53 4.8 8.7 1.0
NE2 X:GLN53 4.9 11.4 1.0
CA X:HIS50 5.0 7.6 1.0

Iron binding site 4 out of 10 in 5fle

Go back to Iron Binding Sites List in 5fle
Iron binding site 4 out of 10 in the High Resolution Ni,Fe-Codh-320 Mv with Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of High Resolution Ni,Fe-Codh-320 Mv with Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1001

b:8.2
occ:1.00
 FE4 X:SF41001 0.0 8.2 1.0
S2 X:SF41001 2.2 8.4 1.0
SG X:CYS56 2.3 8.6 1.0
S1 X:SF41001 2.3 8.0 1.0
S3 X:SF41001 2.3 8.1 1.0
FE2 X:SF41001 2.7 8.0 1.0
FE3 X:SF41001 2.7 8.1 1.0
FE1 X:SF41001 2.7 8.2 1.0
CB X:CYS56 3.2 8.3 1.0
S4 X:SF41001 3.9 8.1 1.0
N X:ILE69 4.0 7.3 1.0
CB X:ILE69 4.4 8.3 1.0
N X:CYS56 4.4 7.8 1.0
CA X:CYS56 4.4 8.2 1.0
CA X:GLY54 4.4 9.0 1.0
N X:GLY54 4.5 9.0 1.0
O X:CYS48 4.6 8.1 1.0
SG X:CYS51 4.6 8.7 1.0
SG X:CYS48 4.7 8.1 1.0
N X:CYS70 4.7 8.4 1.0
CA X:ILE69 4.7 8.3 1.0
CB X:CYS48 4.8 7.7 1.0
SG X:CYS70 4.8 8.3 1.0
CA X:GLY68 4.8 8.2 1.0
C X:GLY68 4.8 8.2 1.0
CG1 X:ILE69 4.9 9.6 1.0

Iron binding site 5 out of 10 in 5fle

Go back to Iron Binding Sites List in 5fle
Iron binding site 5 out of 10 in the High Resolution Ni,Fe-Codh-320 Mv with Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of High Resolution Ni,Fe-Codh-320 Mv with Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1002

b:9.3
occ:1.00
 FE1 X:FES1002 0.0 9.3 1.0
SG X:CYS47 2.3 9.3 1.0
S1 X:FES1002 2.3 9.2 1.0
S2 X:FES1002 2.3 9.8 1.0
FE2 X:FES1002 2.7 9.4 1.0
CB X:CYS47 3.2 8.6 1.0
O X:HOH2129 3.6 13.0 1.0
CA X:CYS47 4.6 7.8 1.0
SG X:CYS39 4.7 10.4 1.0
CB X:PHE41 4.9 9.6 1.0
N X:GLY42 5.0 9.8 1.0
CD X:ARG49 5.0 11.5 1.0

Iron binding site 6 out of 10 in 5fle

Go back to Iron Binding Sites List in 5fle
Iron binding site 6 out of 10 in the High Resolution Ni,Fe-Codh-320 Mv with Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of High Resolution Ni,Fe-Codh-320 Mv with Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1002

b:9.4
occ:1.00
 FE2 X:FES1002 0.0 9.4 1.0
S2 X:FES1002 2.3 9.8 1.0
SG X:CYS39 2.3 10.4 1.0
S1 X:FES1002 2.3 9.2 1.0
FE1 X:FES1002 2.7 9.3 1.0
CB X:CYS39 3.2 9.8 1.0
N X:GLY42 4.2 9.8 1.0
CB X:PHE41 4.4 9.6 1.0
CA X:CYS39 4.6 9.9 1.0
CA X:GLY42 4.8 10.2 1.0
CD2 X:PHE41 4.8 11.5 1.0
SG X:CYS47 4.8 9.3 1.0

Iron binding site 7 out of 10 in 5fle

Go back to Iron Binding Sites List in 5fle
Iron binding site 7 out of 10 in the High Resolution Ni,Fe-Codh-320 Mv with Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of High Resolution Ni,Fe-Codh-320 Mv with Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1003

b:11.9
occ:0.72
 FE1 X:82N1003 0.0 11.9 0.7
S2 X:82N1003 2.3 13.2 0.7
S4 X:82N1003 2.3 12.5 0.8
S3 X:82N1003 2.3 12.2 0.8
SG X:CYS476 2.3 19.4 1.0
FE4 X:82N1003 2.7 11.2 0.8
FE3 X:82N1003 2.7 10.8 0.7
CB X:CYS476 3.4 14.8 1.0
FE X:FE21004 3.5 11.1 0.7
NI X:82N1003 3.6 10.2 0.6
N X:CYS476 3.9 10.3 1.0
O X:HOH2432 3.9 17.3 1.0
S1 X:82N1003 4.0 11.9 0.8
CA X:CYS446 4.1 10.5 1.0
CA X:CYS476 4.3 12.0 1.0
CB X:SER312 4.3 16.4 1.0
OG X:SER312 4.4 16.0 1.0
CB X:CYS446 4.5 10.6 1.0
O X:GLY445 4.6 11.8 1.0
SG X:CYS526 4.6 13.5 1.0
SG X:CYS446 4.6 12.1 1.0
N X:CYS446 4.6 10.8 1.0
C X:GLY445 4.7 10.3 1.0
SG X:CYS294 4.8 14.1 1.0
SG X:CYS333 4.8 12.3 1.0
C X:GLY475 4.9 9.8 1.0
NE2 X:HIS261 4.9 16.8 1.0

Iron binding site 8 out of 10 in 5fle

Go back to Iron Binding Sites List in 5fle
Iron binding site 8 out of 10 in the High Resolution Ni,Fe-Codh-320 Mv with Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of High Resolution Ni,Fe-Codh-320 Mv with Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1003

b:10.8
occ:0.73
 FE3 X:82N1003 0.0 10.8 0.7
S1 X:82N1003 2.2 11.9 0.8
S4 X:82N1003 2.3 12.5 0.8
S3 X:82N1003 2.3 12.2 0.8
SG X:CYS446 2.3 12.1 1.0
FE4 X:82N1003 2.6 11.2 0.8
FE1 X:82N1003 2.7 11.9 0.7
NI X:82N1003 2.8 10.2 0.6
CB X:CYS446 3.1 10.6 1.0
CA X:CYS446 3.3 10.5 1.0
N X:CYS446 3.5 10.8 1.0
C X:GLY445 4.0 10.3 1.0
S2 X:82N1003 4.0 13.2 0.7
C X:82N1003 4.3 12.6 0.5
SG X:CYS333 4.4 12.3 1.0
CA X:GLY445 4.4 10.9 1.0
CB X:HIS561 4.4 8.4 1.0
FE X:FE21004 4.5 11.1 0.7
O X:GLY445 4.6 11.8 1.0
SG X:CYS476 4.6 19.4 1.0
CE X:MET560 4.7 11.0 1.0
SG X:CYS526 4.7 13.5 1.0
C X:CYS446 4.8 9.3 1.0
N X:HIS561 4.9 8.6 1.0

Iron binding site 9 out of 10 in 5fle

Go back to Iron Binding Sites List in 5fle
Iron binding site 9 out of 10 in the High Resolution Ni,Fe-Codh-320 Mv with Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of High Resolution Ni,Fe-Codh-320 Mv with Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1003

b:11.2
occ:0.75
 FE4 X:82N1003 0.0 11.2 0.8
SG X:CYS333 2.2 12.3 1.0
S3 X:82N1003 2.3 12.2 0.8
S2 X:82N1003 2.4 13.2 0.7
S1 X:82N1003 2.4 11.9 0.8
FE3 X:82N1003 2.6 10.8 0.7
FE1 X:82N1003 2.7 11.9 0.7
CB X:CYS333 3.1 11.9 1.0
NI X:82N1003 3.3 10.2 0.6
CE1 X:HIS261 3.5 15.3 1.0
FE X:FE21004 3.5 11.1 0.7
S4 X:82N1003 3.6 12.5 0.8
NE2 X:HIS261 3.7 16.8 1.0
NZ X:LYS563 4.1 11.7 1.0
C X:82N1003 4.2 12.6 0.5
CA X:CYS333 4.5 11.3 1.0
SG X:CYS446 4.6 12.1 1.0
O X:HOH2444 4.6 16.7 1.0
ND1 X:HIS261 4.7 14.2 1.0
CE X:MET560 4.8 11.0 1.0
SG X:CYS476 4.8 19.4 1.0
CE X:LYS563 4.8 10.9 1.0
CB X:HIS561 4.8 8.4 1.0
SG X:CYS526 5.0 13.5 1.0
CD2 X:HIS561 5.0 9.1 1.0

Iron binding site 10 out of 10 in 5fle

Go back to Iron Binding Sites List in 5fle
Iron binding site 10 out of 10 in the High Resolution Ni,Fe-Codh-320 Mv with Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of High Resolution Ni,Fe-Codh-320 Mv with Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1004

b:11.1
occ:0.65
 NE2 X:HIS261 2.0 16.8 1.0
SG X:CYS295 2.3 14.8 0.8
S2 X:82N1003 2.3 13.2 0.7
SG X:CYS295 2.3 15.9 0.2
SG X:CYS526 2.5 13.5 1.0
NI X:82N1003 2.7 10.2 0.6
CE1 X:HIS261 3.0 15.3 1.0
CD2 X:HIS261 3.1 13.1 1.0
CB X:CYS295 3.3 13.8 0.2
CB X:CYS295 3.4 11.1 0.8
C X:82N1003 3.5 12.6 0.5
CB X:CYS526 3.5 10.2 1.0
S4 X:82N1003 3.5 12.5 0.8
FE4 X:82N1003 3.5 11.2 0.8
FE1 X:82N1003 3.5 11.9 0.7
S1 X:82N1003 4.0 11.9 0.8
O X:HOH2432 4.1 17.3 1.0
N X:82N1003 4.1 10.9 0.5
ND1 X:HIS261 4.1 14.2 1.0
CG X:HIS261 4.2 13.0 1.0
N X:CYS526 4.3 9.3 1.0
CA X:CYS295 4.4 11.1 0.8
N X:CYS295 4.4 9.8 0.8
CA X:CYS295 4.4 11.2 0.2
N X:CYS295 4.4 10.3 0.2
FE3 X:82N1003 4.5 10.8 0.7
CA X:CYS526 4.5 10.2 1.0
NZ X:LYS563 4.5 11.7 1.0
CA X:GLY475 4.5 9.4 1.0
O X:HOH2602 4.8 11.6 1.0
SG X:CYS333 5.0 12.3 1.0

Reference:

A.Ciaccafava, D.Tombolelli, L.Domnik, J.Fesseler, J.H.Jeoung, H.Dobbek, M.A.Mroginski, I.Zebger, P.Hildebrandt. When the Inhibitor Tells More Than the Substrate: the Cyanide-Bound State of A Carbon Monoxide Dehydrogenase. Chem Sci V. 7 3162 2016.
ISSN: ISSN 2041-6520
PubMed: 29997808
DOI: 10.1039/C5SC04554A
Page generated: Tue Aug 6 00:59:13 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy