Atomistry » Iron » PDB 6qgr-6r2o » 6qgr
Atomistry »
  Iron »
    PDB 6qgr-6r2o »
      6qgr »

Iron in PDB 6qgr: The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State

Enzymatic activity of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State

All present enzymatic activity of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State:
1.12.98.1;

Protein crystallography data

The structure of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State, PDB code: 6qgr was solved by Y.Ilina, C.Lorent, S.Katz, J.H.Jeoung, S.Shima, M.Horch, I.Zebger, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.14 / 1.84
Space group F 2 3
Cell size a, b, c (Å), α, β, γ (°) 235.826, 235.826, 235.826, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22.1

Other elements in 6qgr:

The structure of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Magnesium (Mg) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Iron atom in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State (pdb code 6qgr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 19 binding sites of Iron where determined in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State, PDB code: 6qgr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 19 in 6qgr

Go back to Iron Binding Sites List in 6qgr
Iron binding site 1 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:32.7
occ:1.00
 FE1 G:SF4301 0.0 32.7 1.0
S2 G:SF4301 2.3 34.9 1.0
SG G:CYS31 2.3 34.5 1.0
S4 G:SF4301 2.3 34.4 1.0
S3 G:SF4301 2.4 35.0 1.0
FE3 G:SF4301 2.7 34.0 1.0
FE4 G:SF4301 2.7 35.6 1.0
FE2 G:SF4301 2.8 34.7 1.0
CB G:CYS31 3.2 26.9 1.0
N G:CYS31 3.8 33.5 1.0
S1 G:SF4301 3.9 36.2 1.0
NE2 A:HIS162 3.9 31.9 1.0
CA G:CYS31 4.0 32.7 1.0
N G:GLY33 4.2 32.8 1.0
CA G:GLY33 4.4 31.6 1.0
C G:CYS31 4.5 34.7 1.0
N G:CYS34 4.5 33.8 1.0
CE1 A:HIS162 4.6 33.8 1.0
N G:THR32 4.6 34.6 1.0
SG G:CYS106 4.7 34.9 1.0
C G:GLY33 4.8 34.4 1.0
SG G:CYS34 4.9 34.6 1.0
SG G:CYS145 4.9 34.3 1.0
C G:GLY30 4.9 35.8 1.0
O A:ARG61 4.9 31.9 1.0
CD2 A:HIS162 5.0 30.1 1.0

Iron binding site 2 out of 19 in 6qgr

Go back to Iron Binding Sites List in 6qgr
Iron binding site 2 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:34.7
occ:1.00
 FE2 G:SF4301 0.0 34.7 1.0
SG G:CYS106 2.2 34.9 1.0
S3 G:SF4301 2.4 35.0 1.0
S1 G:SF4301 2.4 36.2 1.0
S4 G:SF4301 2.5 34.4 1.0
FE3 G:SF4301 2.8 34.0 1.0
FE1 G:SF4301 2.8 32.7 1.0
FE4 G:SF4301 2.9 35.6 1.0
CB G:CYS106 3.2 35.8 1.0
O G:HOH448 3.7 33.0 1.0
N G:CYS106 3.8 30.9 1.0
ND2 G:ASN111 3.8 34.3 1.0
S2 G:SF4301 4.0 34.9 1.0
CA G:CYS106 4.1 33.5 1.0
O A:HOH797 4.5 33.8 1.0
SG G:CYS145 4.7 34.3 1.0
N G:CYS31 4.7 33.5 1.0
CG G:ASN111 4.8 37.6 1.0
SG G:CYS31 4.9 34.5 1.0
SG G:CYS34 4.9 34.6 1.0
CA G:GLY30 5.0 35.0 1.0
C G:SER105 5.0 33.5 1.0

Iron binding site 3 out of 19 in 6qgr

Go back to Iron Binding Sites List in 6qgr
Iron binding site 3 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:34.0
occ:1.00
 FE3 G:SF4301 0.0 34.0 1.0
S2 G:SF4301 2.3 34.9 1.0
SG G:CYS145 2.4 34.3 1.0
S4 G:SF4301 2.4 34.4 1.0
S1 G:SF4301 2.5 36.2 1.0
FE1 G:SF4301 2.7 32.7 1.0
FE2 G:SF4301 2.8 34.7 1.0
FE4 G:SF4301 2.9 35.6 1.0
CB G:CYS145 3.3 33.3 1.0
CA G:CYS145 3.7 31.1 1.0
ND2 G:ASN111 3.8 34.3 1.0
NE2 A:HIS162 3.8 31.9 1.0
S3 G:SF4301 4.0 35.0 1.0
CD2 A:HIS162 4.2 30.1 1.0
CG A:ARG61 4.3 35.3 1.0
C G:CYS145 4.4 36.4 1.0
SG G:CYS106 4.5 34.9 1.0
CA G:PRO146 4.6 34.8 1.0
O G:GLY144 4.7 34.1 1.0
SG G:CYS31 4.7 34.5 1.0
N G:PRO146 4.8 36.0 1.0
CG G:ASN111 4.8 37.6 1.0
NE A:ARG61 4.9 38.7 1.0
CE1 A:HIS162 4.9 33.8 1.0
N G:CYS145 4.9 33.3 1.0

Iron binding site 4 out of 19 in 6qgr

Go back to Iron Binding Sites List in 6qgr
Iron binding site 4 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:35.6
occ:1.00
 FE4 G:SF4301 0.0 35.6 1.0
S1 G:SF4301 2.2 36.2 1.0
SG G:CYS34 2.3 34.6 1.0
S3 G:SF4301 2.4 35.0 1.0
S2 G:SF4301 2.4 34.9 1.0
FE1 G:SF4301 2.7 32.7 1.0
FE3 G:SF4301 2.9 34.0 1.0
FE2 G:SF4301 2.9 34.7 1.0
CB G:CYS34 3.6 38.5 1.0
O G:HOH448 3.6 33.0 1.0
N G:CYS34 3.7 33.8 1.0
CA G:CYS34 4.0 38.4 1.0
S4 G:SF4301 4.1 34.4 1.0
CD G:PRO147 4.1 38.9 1.0
C G:GLY33 4.5 34.4 1.0
CA G:GLY104 4.5 33.0 1.0
SG G:CYS31 4.7 34.5 1.0
O G:GLY144 4.8 34.1 1.0
N G:SER105 4.9 36.4 1.0
CG G:PRO147 4.9 34.7 1.0
OE2 G:GLU76 4.9 42.5 1.0
CA G:GLY33 5.0 31.6 1.0
SG G:CYS106 5.0 34.9 1.0

Iron binding site 5 out of 19 in 6qgr

Go back to Iron Binding Sites List in 6qgr
Iron binding site 5 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe302

b:32.8
occ:1.00
 FE1 G:SF4302 0.0 32.8 1.0
S4 G:SF4302 2.3 33.3 1.0
SG G:CYS234 2.3 33.1 1.0
S2 G:SF4302 2.3 34.0 1.0
S3 G:SF4302 2.4 34.4 1.0
FE3 G:SF4302 2.7 33.4 1.0
FE4 G:SF4302 2.8 33.9 1.0
FE2 G:SF4302 2.8 34.5 1.0
CB G:CYS234 3.1 32.2 1.0
CA G:CYS234 3.6 33.4 1.0
N G:PHE192 3.7 33.8 1.0
S1 G:SF4302 3.9 33.2 1.0
N G:LYS236 4.0 36.8 1.0
N G:ILE235 4.1 28.6 1.0
C G:CYS234 4.2 31.8 1.0
CA G:PHE192 4.3 34.0 1.0
CB G:PHE192 4.5 28.9 1.0
C G:CYS191 4.5 38.6 1.0
CA G:LYS236 4.5 32.5 1.0
N G:CYS237 4.6 32.9 1.0
CA G:CYS191 4.8 33.9 1.0
SG G:CYS215 4.9 31.2 1.0
N G:CYS234 4.9 33.0 1.0
SG G:CYS240 4.9 32.4 1.0
C G:ILE235 5.0 35.9 1.0

Iron binding site 6 out of 19 in 6qgr

Go back to Iron Binding Sites List in 6qgr
Iron binding site 6 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe302

b:34.5
occ:1.00
 FE2 G:SF4302 0.0 34.5 1.0
S1 G:SF4302 2.3 33.2 1.0
SG G:CYS240 2.3 32.4 1.0
S3 G:SF4302 2.3 34.4 1.0
S4 G:SF4302 2.4 33.3 1.0
FE4 G:SF4302 2.8 33.9 1.0
FE1 G:SF4302 2.8 32.8 1.0
FE3 G:SF4302 2.9 33.4 1.0
CB G:CYS240 3.3 35.8 1.0
N G:CYS240 3.8 33.7 1.0
N G:PHE192 3.9 33.8 1.0
S2 G:SF4302 4.0 34.0 1.0
CA G:PHE192 4.1 34.0 1.0
CA G:CYS240 4.2 33.0 1.0
CD1 G:ILE220 4.2 28.4 1.0
O G:HOH477 4.2 35.8 1.0
C G:CYS191 4.3 38.6 1.0
O G:CYS191 4.6 34.9 1.0
N G:SER239 4.7 34.2 1.0
CB G:PHE192 4.8 28.9 1.0
SG G:CYS234 4.8 33.1 1.0
SG G:CYS237 4.8 33.2 1.0
SG G:CYS215 4.9 31.2 1.0
C G:SER239 5.0 35.7 1.0
N G:GLY238 5.0 34.5 1.0

Iron binding site 7 out of 19 in 6qgr

Go back to Iron Binding Sites List in 6qgr
Iron binding site 7 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe302

b:33.4
occ:1.00
 FE3 G:SF4302 0.0 33.4 1.0
SG G:CYS215 2.3 31.2 1.0
S4 G:SF4302 2.3 33.3 1.0
S2 G:SF4302 2.3 34.0 1.0
S1 G:SF4302 2.4 33.2 1.0
FE1 G:SF4302 2.7 32.8 1.0
FE4 G:SF4302 2.9 33.9 1.0
FE2 G:SF4302 2.9 34.5 1.0
CB G:CYS215 3.3 31.7 1.0
CA G:CYS215 3.8 33.2 1.0
CD G:PRO216 4.0 32.3 1.0
S3 G:SF4302 4.1 34.4 1.0
CB G:ALA219 4.3 34.0 1.0
CG2 G:VAL217 4.4 30.0 1.0
C G:CYS215 4.5 31.5 1.0
CD1 G:ILE220 4.5 28.4 1.0
N G:PRO216 4.6 33.6 1.0
CG1 G:ILE220 4.7 31.3 1.0
SG G:CYS237 4.8 33.2 1.0
SG G:CYS234 4.9 33.1 1.0
SG G:CYS240 4.9 32.4 1.0
CA G:CYS234 5.0 33.4 1.0
CB G:CYS234 5.0 32.2 1.0
CG G:PRO216 5.0 29.7 1.0
N G:ALA219 5.0 33.3 1.0

Iron binding site 8 out of 19 in 6qgr

Go back to Iron Binding Sites List in 6qgr
Iron binding site 8 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe302

b:33.9
occ:1.00
 FE4 G:SF4302 0.0 33.9 1.0
S1 G:SF4302 2.3 33.2 1.0
SG G:CYS237 2.3 33.2 1.0
S3 G:SF4302 2.3 34.4 1.0
S2 G:SF4302 2.4 34.0 1.0
FE1 G:SF4302 2.8 32.8 1.0
FE2 G:SF4302 2.8 34.5 1.0
FE3 G:SF4302 2.9 33.4 1.0
CB G:CYS237 3.5 29.1 1.0
N G:CYS237 3.6 32.9 1.0
N G:GLY238 3.9 34.5 1.0
CA G:CYS237 3.9 35.0 1.0
S4 G:SF4302 4.0 33.3 1.0
N G:SER239 4.0 34.2 1.0
CD G:PRO216 4.1 32.3 1.0
C G:CYS237 4.2 35.0 1.0
CB G:SER239 4.4 36.3 1.0
OG G:SER239 4.6 35.2 1.0
N G:LYS236 4.7 36.8 1.0
C G:LYS236 4.7 37.4 1.0
N G:CYS240 4.7 33.7 1.0
CG G:PRO216 4.7 29.7 1.0
CA G:SER239 4.8 29.5 1.0
SG G:CYS234 4.8 33.1 1.0
CA G:GLY238 4.8 31.3 1.0
SG G:CYS215 4.8 31.2 1.0
C G:GLY238 4.9 35.8 1.0
SG G:CYS240 4.9 32.4 1.0
CG1 G:ILE235 4.9 31.0 1.0
CA G:LYS236 4.9 32.5 1.0

Iron binding site 9 out of 19 in 6qgr

Go back to Iron Binding Sites List in 6qgr
Iron binding site 9 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe303

b:34.3
occ:1.00
 FE1 G:SF4303 0.0 34.3 1.0
SG G:CYS211 2.3 34.8 1.0
S4 G:SF4303 2.3 35.9 1.0
S2 G:SF4303 2.3 35.9 1.0
S3 G:SF4303 2.4 39.1 1.0
FE4 G:SF4303 2.8 35.4 1.0
FE3 G:SF4303 2.9 35.9 1.0
FE2 G:SF4303 2.9 35.5 1.0
CB G:CYS211 3.3 32.9 1.0
CG G:PRO227 3.8 33.7 1.0
N G:CYS211 3.9 31.2 1.0
S1 G:SF4303 4.1 36.2 1.0
CA G:CYS211 4.2 31.6 1.0
N G:THR210 4.5 35.4 1.0
N G:GLY209 4.5 30.1 1.0
CA G:GLY209 4.6 39.3 1.0
CD1 G:LEU195 4.7 29.0 1.0
SG G:CYS208 4.7 37.1 1.0
C G:GLY209 4.7 38.6 1.0
SG G:CYS205 4.9 34.7 1.0
SG G:CYS244 4.9 35.4 1.0
CB G:PRO227 4.9 33.9 1.0
CD G:PRO227 4.9 35.6 1.0
CD2 G:LEU195 5.0 36.5 1.0

Iron binding site 10 out of 19 in 6qgr

Go back to Iron Binding Sites List in 6qgr
Iron binding site 10 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe303

b:35.5
occ:1.00
 FE2 G:SF4303 0.0 35.5 1.0
SG G:CYS205 2.3 34.7 1.0
S3 G:SF4303 2.3 39.1 1.0
S4 G:SF4303 2.4 35.9 1.0
S1 G:SF4303 2.4 36.2 1.0
FE4 G:SF4303 2.8 35.4 1.0
FE1 G:SF4303 2.9 34.3 1.0
FE3 G:SF4303 2.9 35.9 1.0
CB G:CYS205 3.3 38.6 1.0
CA G:CYS205 3.7 35.2 1.0
N G:GLY207 3.9 37.4 1.0
N G:MET206 4.0 30.8 1.0
CG G:PRO227 4.1 33.7 1.0
S2 G:SF4303 4.1 35.9 1.0
C G:CYS205 4.2 33.9 1.0
CG1 G:VAL199 4.4 33.0 1.0
CD G:PRO227 4.4 35.6 1.0
CA G:GLY207 4.6 33.6 1.0
N G:CYS208 4.9 33.0 1.0
C G:MET206 4.9 29.9 1.0
SG G:CYS244 5.0 35.4 1.0

Reference:

Y.Ilina, C.Lorent, S.Katz, J.H.Jeoung, S.Shima, M.Horch, I.Zebger, H.Dobbek. X-Ray Crystallography and Vibrational Spectroscopy Reveal the Key Determinants of Biocatalytic Dihydrogen Cycling By [Nife] Hydrogenases. Angew.Chem.Int.Ed.Engl. 2019.
ISSN: ESSN 1521-3773
PubMed: 31591784
DOI: 10.1002/ANIE.201908258
Page generated: Wed Aug 7 07:53:12 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy