Atomistry » Iron » PDB 5qj3-5tdt » 5t5m
Atomistry »
  Iron »
    PDB 5qj3-5tdt »
      5t5m »

Iron in PDB 5t5m: Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.

Enzymatic activity of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.

All present enzymatic activity of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.:
1.2.99.5;

Protein crystallography data

The structure of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A., PDB code: 5t5m was solved by T.Wagner, U.Ermler, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.22 / 2.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.543, 105.543, 340.549, 90.00, 90.00, 120.00
R / Rfree (%) 15.8 / 18.2

Other elements in 5t5m:

The structure of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. also contains other interesting chemical elements:

Tungsten (W) 1 atom
Magnesium (Mg) 3 atoms
Potassium (K) 1 atom
Zinc (Zn) 2 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 44;

Binding sites:

The binding sites of Iron atom in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. (pdb code 5t5m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 44 binding sites of Iron where determined in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A., PDB code: 5t5m:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 44 in 5t5m

Go back to Iron Binding Sites List in 5t5m
Iron binding site 1 out of 44 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:60.5
occ:1.00
FE1 B:SF4502 0.0 60.5 1.0
S3 B:SF4502 2.0 50.4 1.0
S4 B:SF4502 2.0 61.1 1.0
S2 B:SF4502 2.1 63.7 1.0
SG B:CYS16 2.5 64.2 1.0
FE3 B:SF4502 2.8 67.9 1.0
FE4 B:SF4502 2.9 59.4 1.0
FE2 B:SF4502 3.0 58.4 1.0
CB B:CYS16 3.2 67.5 1.0
S1 B:SF4502 3.6 57.3 1.0
N B:CYS16 3.9 61.4 1.0
CD B:ARG159 4.0 63.3 1.0
CA B:CYS16 4.1 65.5 1.0
CB B:THR14 4.3 55.4 1.0
CG2 B:THR14 4.3 53.9 1.0
NH1 B:ARG159 4.4 64.2 1.0
CB B:ARG159 4.5 62.6 1.0
CG B:ARG159 4.5 62.8 1.0
CB B:CYS9 4.6 67.6 1.0
N B:LEU15 4.9 56.4 1.0
SG B:CYS9 4.9 68.1 1.0

Iron binding site 2 out of 44 in 5t5m

Go back to Iron Binding Sites List in 5t5m
Iron binding site 2 out of 44 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:58.4
occ:1.00
FE2 B:SF4502 0.0 58.4 1.0
S4 B:SF4502 2.0 61.1 1.0
S3 B:SF4502 2.1 50.4 1.0
S1 B:SF4502 2.1 57.3 1.0
SG B:CYS12 2.5 69.3 1.0
FE3 B:SF4502 2.8 67.9 1.0
FE4 B:SF4502 2.9 59.4 1.0
FE1 B:SF4502 3.0 60.5 1.0
CB B:CYS12 3.1 65.8 1.0
S2 B:SF4502 3.6 63.7 1.0
N B:CYS12 3.7 62.0 1.0
CA B:CYS12 3.9 62.7 1.0
CB B:THR14 4.1 55.4 1.0
C B:CYS12 4.2 62.0 1.0
O B:CYS12 4.3 63.7 1.0
OG1 B:THR14 4.4 57.3 1.0
CD B:PRO158 4.5 50.5 1.0
CD2 B:PHE11 4.5 65.9 1.0
N B:THR14 4.7 54.9 1.0
SG B:CYS35 4.8 65.0 1.0
CB B:PHE11 4.8 65.0 1.0
C B:PHE11 4.9 60.4 1.0
N B:LEU15 5.0 56.4 1.0
CA B:THR14 5.0 54.7 1.0
SG B:CYS9 5.0 68.1 1.0
CA B:HIS157 5.0 52.2 1.0

Iron binding site 3 out of 44 in 5t5m

Go back to Iron Binding Sites List in 5t5m
Iron binding site 3 out of 44 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:67.9
occ:1.00
FE3 B:SF4502 0.0 67.9 1.0
S2 B:SF4502 2.0 63.7 1.0
S1 B:SF4502 2.0 57.3 1.0
S4 B:SF4502 2.0 61.1 1.0
SG B:CYS35 2.4 65.0 1.0
FE4 B:SF4502 2.8 59.4 1.0
FE1 B:SF4502 2.8 60.5 1.0
FE2 B:SF4502 2.8 58.4 1.0
CB B:CYS35 3.3 66.8 1.0
S3 B:SF4502 3.4 50.4 1.0
N B:CYS35 4.0 65.9 1.0
CD B:PRO158 4.1 50.5 1.0
CD B:ARG159 4.2 63.3 1.0
CA B:CYS35 4.2 66.6 1.0
CG B:ARG159 4.2 62.8 1.0
N B:GLY38 4.4 63.7 1.0
CG B:PRO158 4.6 51.4 1.0
N B:ARG159 4.6 60.5 1.0
CB B:PRO158 4.7 53.0 1.0
N B:PRO158 4.7 50.6 1.0
CA B:GLY38 4.7 63.5 1.0
CB B:ARG159 4.8 62.6 1.0
C B:CYS35 4.9 66.6 1.0

Iron binding site 4 out of 44 in 5t5m

Go back to Iron Binding Sites List in 5t5m
Iron binding site 4 out of 44 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:59.4
occ:1.00
FE4 B:SF4502 0.0 59.4 1.0
S2 B:SF4502 2.0 63.7 1.0
S1 B:SF4502 2.1 57.3 1.0
S3 B:SF4502 2.1 50.4 1.0
SG B:CYS9 2.4 68.1 1.0
FE3 B:SF4502 2.8 67.9 1.0
FE1 B:SF4502 2.9 60.5 1.0
FE2 B:SF4502 2.9 58.4 1.0
CB B:CYS9 3.2 67.6 1.0
S4 B:SF4502 3.4 61.1 1.0
CA B:GLY38 4.0 63.5 1.0
CB B:PHE11 4.3 65.0 1.0
N B:GLY38 4.4 63.7 1.0
CA B:CYS9 4.6 67.8 1.0
N B:CYS12 4.6 62.0 1.0
SG B:CYS35 4.6 65.0 1.0
N B:PHE11 4.7 64.0 1.0
C B:CYS9 4.9 67.2 1.0
O B:CYS9 4.9 63.2 1.0
CA B:PHE11 5.0 62.5 1.0

Iron binding site 5 out of 44 in 5t5m

Go back to Iron Binding Sites List in 5t5m
Iron binding site 5 out of 44 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:56.1
occ:1.00
FE1 F:SF4501 0.0 56.1 1.0
S2 F:SF4501 2.0 41.5 1.0
S3 F:SF4501 2.0 50.1 1.0
S4 F:SF4501 2.1 49.9 1.0
SG F:CYS204 2.4 58.5 1.0
FE2 F:SF4501 3.0 53.4 1.0
FE4 F:SF4501 3.0 51.5 1.0
CB F:CYS204 3.1 59.6 1.0
FE3 F:SF4501 3.1 53.4 1.0
CA F:CYS204 3.6 60.0 1.0
S1 F:SF4501 3.8 51.1 1.0
CD F:PRO205 3.8 62.7 1.0
CB F:ALA208 4.3 59.9 1.0
C F:CYS204 4.4 62.0 1.0
CD1 F:ILE209 4.4 62.4 1.0
N F:PRO205 4.4 62.3 1.0
CG1 F:ILE209 4.4 64.9 1.0
CG2 F:VAL206 4.4 60.1 1.0
N F:ALA208 4.8 60.2 1.0
N F:CYS204 4.8 59.4 1.0
SG F:CYS157 4.9 56.1 1.0
CG F:PRO205 4.9 64.7 1.0
N F:VAL206 5.0 62.6 1.0

Iron binding site 6 out of 44 in 5t5m

Go back to Iron Binding Sites List in 5t5m
Iron binding site 6 out of 44 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:53.4
occ:1.00
FE2 F:SF4501 0.0 53.4 1.0
S1 F:SF4501 2.0 51.1 1.0
S4 F:SF4501 2.1 49.9 1.0
S3 F:SF4501 2.1 50.1 1.0
SG F:CYS157 2.5 56.1 1.0
FE4 F:SF4501 2.8 51.5 1.0
FE3 F:SF4501 2.8 53.4 1.0
FE1 F:SF4501 3.0 56.1 1.0
S2 F:SF4501 3.3 41.5 1.0
N F:CYS157 3.4 57.0 1.0
CB F:CYS157 3.6 57.3 1.0
N F:GLY158 3.6 58.8 1.0
CA F:CYS157 3.9 56.4 1.0
CD F:PRO205 4.1 62.7 1.0
C F:CYS157 4.1 56.9 1.0
N F:MET159 4.2 56.3 1.0
N F:TYR156 4.3 53.5 1.0
C F:TYR156 4.3 57.1 1.0
CA F:TYR156 4.5 56.0 1.0
CA F:GLY158 4.6 59.5 1.0
CG F:PRO205 4.7 64.7 1.0
CG1 F:ILE155 4.8 53.6 1.0
N F:CYS160 4.9 57.6 1.0
C F:GLY158 4.9 60.3 1.0
SG F:CYS154 5.0 53.9 1.0
SG F:CYS160 5.0 62.2 1.0

Iron binding site 7 out of 44 in 5t5m

Go back to Iron Binding Sites List in 5t5m
Iron binding site 7 out of 44 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:53.4
occ:1.00
FE3 F:SF4501 0.0 53.4 1.0
S4 F:SF4501 2.0 49.9 1.0
S1 F:SF4501 2.0 51.1 1.0
S2 F:SF4501 2.1 41.5 1.0
SG F:CYS154 2.4 53.9 1.0
FE2 F:SF4501 2.8 53.4 1.0
FE4 F:SF4501 3.0 51.5 1.0
FE1 F:SF4501 3.1 56.1 1.0
CB F:CYS154 3.3 59.0 1.0
S3 F:SF4501 3.6 50.1 1.0
N F:TYR156 3.6 53.5 1.0
CA F:CYS154 3.7 59.9 1.0
N F:ILE155 3.9 52.4 1.0
CA F:TYR156 4.1 56.0 1.0
C F:CYS154 4.2 56.5 1.0
CD1 F:ILE187 4.2 59.7 1.0
N F:CYS157 4.6 57.0 1.0
C F:ILE155 4.6 52.8 1.0
C F:TYR156 4.8 57.1 1.0
CA F:ILE155 4.9 52.9 1.0
CB F:ALA208 4.9 59.9 1.0

Iron binding site 8 out of 44 in 5t5m

Go back to Iron Binding Sites List in 5t5m
Iron binding site 8 out of 44 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:51.5
occ:1.00
FE4 F:SF4501 0.0 51.5 1.0
S3 F:SF4501 2.0 50.1 1.0
S2 F:SF4501 2.1 41.5 1.0
S1 F:SF4501 2.1 51.1 1.0
SG F:CYS160 2.5 62.2 1.0
FE2 F:SF4501 2.8 53.4 1.0
FE3 F:SF4501 3.0 53.4 1.0
FE1 F:SF4501 3.0 56.1 1.0
CB F:CYS160 3.1 58.9 1.0
S4 F:SF4501 3.5 49.9 1.0
N F:CYS160 3.9 57.6 1.0
CD1 F:ILE187 4.0 59.7 1.0
CA F:CYS160 4.1 57.2 1.0
CD1 F:ILE209 4.2 62.4 1.0
N F:MET159 4.8 56.3 1.0
SG F:CYS157 4.9 56.1 1.0
N F:GLY158 4.9 58.8 1.0
CG1 F:ILE209 5.0 64.9 1.0
N F:GLU161 5.0 58.2 1.0

Iron binding site 9 out of 44 in 5t5m

Go back to Iron Binding Sites List in 5t5m
Iron binding site 9 out of 44 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:52.1
occ:1.00
FE1 F:SF4502 0.0 52.1 1.0
S3 F:SF4502 2.0 52.1 1.0
S2 F:SF4502 2.0 46.8 1.0
S4 F:SF4502 2.2 49.1 1.0
SG F:CYS197 2.4 58.1 1.0
FE4 F:SF4502 2.9 53.5 1.0
FE2 F:SF4502 3.0 50.2 1.0
FE3 F:SF4502 3.0 53.7 1.0
N F:CYS197 3.3 51.5 1.0
CB F:CYS197 3.5 55.7 1.0
N F:GLY198 3.7 61.2 1.0
S1 F:SF4502 3.7 53.6 1.0
CA F:CYS197 3.8 52.9 1.0
C F:CYS197 4.1 54.7 1.0
CD F:PRO165 4.2 55.3 1.0
N F:ILE199 4.2 58.1 1.0
N F:HIS196 4.3 56.0 1.0
C F:HIS196 4.4 54.1 1.0
CA F:HIS196 4.5 56.0 1.0
CG F:PRO165 4.6 56.3 1.0
CA F:GLY198 4.7 64.8 1.0
CB F:ILE199 4.7 51.0 1.0
CG2 F:VAL195 4.8 54.5 1.0
C F:GLY198 4.9 63.4 1.0
N F:CYS200 4.9 58.4 1.0
SG F:CYS200 4.9 62.2 1.0

Iron binding site 10 out of 44 in 5t5m

Go back to Iron Binding Sites List in 5t5m
Iron binding site 10 out of 44 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:50.2
occ:1.00
FE2 F:SF4502 0.0 50.2 1.0
S4 F:SF4502 2.0 49.1 1.0
S1 F:SF4502 2.1 53.6 1.0
S3 F:SF4502 2.1 52.1 1.0
SG F:CYS164 2.4 52.5 1.0
FE3 F:SF4502 2.8 53.7 1.0
FE1 F:SF4502 3.0 52.1 1.0
FE4 F:SF4502 3.0 53.5 1.0
CB F:CYS164 3.3 55.8 1.0
S2 F:SF4502 3.6 46.8 1.0
CA F:CYS164 3.8 58.1 1.0
CD F:PRO165 3.9 55.3 1.0
CG2 F:VAL166 4.3 53.2 1.0
CB F:ALA168 4.3 59.1 1.0
C F:CYS164 4.5 58.7 1.0
N F:PRO165 4.5 56.0 1.0
CD1 F:ILE169 4.6 52.5 1.0
CG1 F:ILE169 4.8 53.5 1.0
CG F:PRO165 4.9 56.3 1.0
N F:ALA168 4.9 60.8 1.0
SG F:CYS197 5.0 58.1 1.0
N F:CYS164 5.0 59.8 1.0

Reference:

T.Wagner, U.Ermler, S.Shima. The Methanogenic CO2 Reducing-and-Fixing Enzyme Is Bifunctional and Contains 46 [4FE-4S] Clusters. Science V. 354 114 2016.
ISSN: ESSN 1095-9203
PubMed: 27846502
DOI: 10.1126/SCIENCE.AAF9284
Page generated: Sun Dec 13 16:12:04 2020

Last articles

Zn in 7L0B
Zn in 7KZZ
Zn in 7KZL
Zn in 7L3O
Zn in 7L52
Zn in 7L6T
Zn in 7KZ7
Zn in 7L6R
Zn in 7KKM
Zn in 7KKQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy