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Cobalt in PDB 9grd: Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site

Enzymatic activity of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site

All present enzymatic activity of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site:
5.3.1.5;

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site (pdb code 9grd). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site, PDB code: 9grd:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 9grd

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Cobalt binding site 1 out of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co401

b:76.4
occ:1.00
 OD2 A:ASP255 2.2 56.1 1.0
OD1 A:ASP257 2.2 64.9 1.0
NE2 A:HIS220 2.3 58.8 1.0
OD2 A:ASP257 2.8 60.8 1.0
CD2 A:HIS220 2.8 49.7 1.0
CG A:ASP255 2.8 56.8 1.0
CG A:ASP257 2.8 59.3 1.0
OD1 A:ASP255 2.9 61.6 1.0
OE2 A:GLU217 3.0 59.6 1.0
CE1 A:HIS220 3.3 58.9 1.0
CD A:GLU217 3.5 57.7 1.0
ND2 A:ASN247 3.7 51.4 1.0
OE1 A:GLU217 3.8 64.0 1.0
CG A:HIS220 4.0 49.0 1.0
ND1 A:HIS220 4.2 56.4 1.0
CB A:ASP255 4.3 52.2 1.0
CB A:ASP257 4.3 51.9 1.0
CG A:GLU217 4.5 51.6 1.0
OD2 A:ASP287 4.5 68.4 1.0
CE A:LYS183 4.8 46.5 1.0
CA A:ASP257 5.0 50.0 1.0
NZ A:LYS183 5.0 50.9 1.0
CG A:ASN247 5.0 52.2 1.0

Cobalt binding site 2 out of 8 in 9grd

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Cobalt binding site 2 out of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co402

b:93.2
occ:1.00
 OD2 A:ASP287 2.2 68.4 1.0
OE2 A:GLU181 2.2 66.8 1.0
OE1 A:GLU217 2.2 64.0 1.0
OD2 A:ASP245 2.4 67.1 1.0
CD A:GLU217 3.1 57.7 1.0
CD A:GLU181 3.1 60.2 1.0
CG A:ASP287 3.1 63.4 1.0
O A:HOH501 3.3 30.0 1.0
CG A:ASP245 3.5 59.0 1.0
OE2 A:GLU217 3.5 59.6 1.0
OE1 A:GLU181 3.5 64.6 1.0
CB A:ASP287 3.6 56.2 1.0
CB A:ASP245 4.1 50.1 1.0
OD1 A:ASP287 4.2 63.5 1.0
CG A:GLU217 4.3 51.6 1.0
CG A:GLU181 4.3 51.0 1.0
CE1 A:HIS220 4.4 58.9 1.0
OD1 A:ASP245 4.5 56.8 1.0
CB A:GLU217 4.6 47.2 1.0
ND1 A:HIS220 4.9 56.4 1.0
ND2 A:ASN215 5.0 47.7 1.0
NE2 A:HIS220 5.0 58.8 1.0

Cobalt binding site 3 out of 8 in 9grd

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Cobalt binding site 3 out of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co401

b:76.4
occ:1.00
 OD2 B:ASP255 2.2 56.1 1.0
OD1 B:ASP257 2.2 64.9 1.0
NE2 B:HIS220 2.3 58.8 1.0
OD2 B:ASP257 2.8 60.8 1.0
CD2 B:HIS220 2.8 49.7 1.0
CG B:ASP255 2.8 56.8 1.0
CG B:ASP257 2.8 59.3 1.0
OD1 B:ASP255 2.9 61.6 1.0
OE2 B:GLU217 3.0 59.6 1.0
CE1 B:HIS220 3.3 58.9 1.0
CD B:GLU217 3.5 57.7 1.0
ND2 B:ASN247 3.7 51.4 1.0
OE1 B:GLU217 3.8 64.0 1.0
CG B:HIS220 4.0 49.0 1.0
ND1 B:HIS220 4.2 56.4 1.0
CB B:ASP255 4.3 52.2 1.0
CB B:ASP257 4.3 51.9 1.0
CG B:GLU217 4.5 51.6 1.0
OD2 B:ASP287 4.5 68.4 1.0
CE B:LYS183 4.8 46.5 1.0
CA B:ASP257 5.0 50.0 1.0
NZ B:LYS183 5.0 50.9 1.0
CG B:ASN247 5.0 52.2 1.0

Cobalt binding site 4 out of 8 in 9grd

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Cobalt binding site 4 out of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co402

b:93.2
occ:1.00
 OD2 B:ASP287 2.2 68.4 1.0
OE2 B:GLU181 2.2 66.8 1.0
OE1 B:GLU217 2.2 64.0 1.0
OD2 B:ASP245 2.4 67.1 1.0
CD B:GLU217 3.1 57.7 1.0
CD B:GLU181 3.1 60.2 1.0
CG B:ASP287 3.1 63.4 1.0
O B:HOH501 3.3 30.0 1.0
CG B:ASP245 3.5 59.0 1.0
OE2 B:GLU217 3.5 59.6 1.0
OE1 B:GLU181 3.5 64.6 1.0
CB B:ASP287 3.6 56.2 1.0
CB B:ASP245 4.1 50.1 1.0
OD1 B:ASP287 4.2 63.5 1.0
CG B:GLU217 4.3 51.6 1.0
CG B:GLU181 4.3 51.0 1.0
CE1 B:HIS220 4.4 58.9 1.0
OD1 B:ASP245 4.5 56.8 1.0
CB B:GLU217 4.6 47.2 1.0
ND1 B:HIS220 4.9 56.4 1.0
ND2 B:ASN215 5.0 47.7 1.0
NE2 B:HIS220 5.0 58.8 1.0

Cobalt binding site 5 out of 8 in 9grd

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Cobalt binding site 5 out of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co401

b:76.4
occ:1.00
 OD2 C:ASP255 2.2 56.1 1.0
OD1 C:ASP257 2.2 64.9 1.0
NE2 C:HIS220 2.3 58.8 1.0
OD2 C:ASP257 2.8 60.8 1.0
CD2 C:HIS220 2.8 49.7 1.0
CG C:ASP255 2.8 56.8 1.0
CG C:ASP257 2.8 59.3 1.0
OD1 C:ASP255 2.9 61.6 1.0
OE2 C:GLU217 3.0 59.6 1.0
CE1 C:HIS220 3.3 58.9 1.0
CD C:GLU217 3.5 57.7 1.0
ND2 C:ASN247 3.7 51.4 1.0
OE1 C:GLU217 3.8 64.0 1.0
CG C:HIS220 4.0 49.0 1.0
ND1 C:HIS220 4.2 56.4 1.0
CB C:ASP255 4.3 52.2 1.0
CB C:ASP257 4.3 51.9 1.0
CG C:GLU217 4.5 51.6 1.0
OD2 C:ASP287 4.5 68.4 1.0
CE C:LYS183 4.8 46.5 1.0
CA C:ASP257 5.0 50.0 1.0
NZ C:LYS183 5.0 50.9 1.0
CG C:ASN247 5.0 52.2 1.0

Cobalt binding site 6 out of 8 in 9grd

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Cobalt binding site 6 out of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co402

b:93.2
occ:1.00
 OD2 C:ASP287 2.2 68.4 1.0
OE2 C:GLU181 2.2 66.8 1.0
OE1 C:GLU217 2.2 64.0 1.0
OD2 C:ASP245 2.4 67.1 1.0
CD C:GLU217 3.1 57.7 1.0
CD C:GLU181 3.1 60.2 1.0
CG C:ASP287 3.1 63.4 1.0
O C:HOH501 3.4 30.0 1.0
CG C:ASP245 3.5 59.0 1.0
OE2 C:GLU217 3.5 59.6 1.0
OE1 C:GLU181 3.5 64.6 1.0
CB C:ASP287 3.6 56.2 1.0
CB C:ASP245 4.1 50.1 1.0
OD1 C:ASP287 4.2 63.5 1.0
CG C:GLU217 4.3 51.6 1.0
CG C:GLU181 4.3 51.0 1.0
CE1 C:HIS220 4.4 58.9 1.0
OD1 C:ASP245 4.5 56.8 1.0
CB C:GLU217 4.6 47.2 1.0
ND1 C:HIS220 4.9 56.4 1.0
ND2 C:ASN215 5.0 47.7 1.0
NE2 C:HIS220 5.0 58.8 1.0

Cobalt binding site 7 out of 8 in 9grd

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Cobalt binding site 7 out of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co401

b:76.4
occ:1.00
 OD2 D:ASP255 2.2 56.1 1.0
OD1 D:ASP257 2.2 64.9 1.0
NE2 D:HIS220 2.3 58.8 1.0
OD2 D:ASP257 2.8 60.8 1.0
CD2 D:HIS220 2.8 49.7 1.0
CG D:ASP255 2.8 56.8 1.0
CG D:ASP257 2.8 59.3 1.0
OD1 D:ASP255 2.9 61.6 1.0
OE2 D:GLU217 3.0 59.6 1.0
CE1 D:HIS220 3.3 58.9 1.0
CD D:GLU217 3.5 57.7 1.0
ND2 D:ASN247 3.7 51.4 1.0
OE1 D:GLU217 3.8 64.0 1.0
CG D:HIS220 4.0 49.0 1.0
ND1 D:HIS220 4.2 56.4 1.0
CB D:ASP255 4.3 52.2 1.0
CB D:ASP257 4.3 51.9 1.0
CG D:GLU217 4.5 51.6 1.0
OD2 D:ASP287 4.5 68.4 1.0
CE D:LYS183 4.8 46.5 1.0
CA D:ASP257 5.0 50.0 1.0
NZ D:LYS183 5.0 50.9 1.0
CG D:ASN247 5.0 52.2 1.0

Cobalt binding site 8 out of 8 in 9grd

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Cobalt binding site 8 out of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co402

b:93.2
occ:1.00
 OD2 D:ASP287 2.2 68.4 1.0
OE2 D:GLU181 2.2 66.8 1.0
OE1 D:GLU217 2.2 64.0 1.0
OD2 D:ASP245 2.4 67.1 1.0
CD D:GLU217 3.1 57.7 1.0
CD D:GLU181 3.1 60.2 1.0
CG D:ASP287 3.1 63.4 1.0
O D:HOH501 3.3 30.0 1.0
OE2 D:GLU217 3.5 59.6 1.0
CG D:ASP245 3.5 59.0 1.0
OE1 D:GLU181 3.5 64.6 1.0
CB D:ASP287 3.6 56.2 1.0
CB D:ASP245 4.1 50.1 1.0
OD1 D:ASP287 4.2 63.5 1.0
CG D:GLU217 4.3 51.6 1.0
CG D:GLU181 4.3 51.0 1.0
CE1 D:HIS220 4.4 58.9 1.0
OD1 D:ASP245 4.5 56.8 1.0
CB D:GLU217 4.6 47.2 1.0
ND1 D:HIS220 4.9 56.4 1.0
ND2 D:ASN215 5.0 47.7 1.0
NE2 D:HIS220 5.0 58.8 1.0

Reference:

J.Slawek, A.Klonecka, M.Kozak, M.Rawski. Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site To Be Published.
Page generated: Sun Jul 13 22:16:14 2025

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