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Cobalt in PDB 1qt1: Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution

Enzymatic activity of Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution

All present enzymatic activity of Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution:
5.3.1.5;

Protein crystallography data

The structure of Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution, PDB code: 1qt1 was solved by L.Niu, M.Teng, X.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 5.00 / 1.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.976, 98.836, 93.927, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 21.9

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution (pdb code 1qt1). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution, PDB code: 1qt1:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 1qt1

Go back to Cobalt Binding Sites List in 1qt1
Cobalt binding site 1 out of 4 in the Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co400

b:16.1
occ:1.00
 OD2 A:ASP244 1.9 17.6 1.0
OE1 A:GLU216 1.9 3.4 1.0
OD2 A:ASP286 2.1 12.3 1.0
OE2 A:GLU180 2.2 13.0 1.0
CD A:GLU180 2.9 7.9 1.0
CG A:ASP244 3.0 10.2 1.0
CG A:ASP286 3.1 7.2 1.0
CD A:GLU216 3.1 7.0 1.0
OE1 A:GLU180 3.1 10.4 1.0
CB A:ASP286 3.4 8.4 1.0
CB A:ASP244 3.5 8.4 1.0
O A:HOH1288 3.6 18.6 1.0
CG A:GLU216 3.8 4.5 1.0
O A:HOH1290 3.8 36.7 1.0
CB A:GLU216 3.9 3.5 1.0
O A:HOH1635 4.0 45.0 1.0
OD1 A:ASP244 4.0 10.0 1.0
OE2 A:GLU216 4.1 7.5 1.0
OD1 A:ASP286 4.2 9.3 1.0
CE1 A:HIS219 4.2 4.6 1.0
CG A:GLU180 4.2 6.9 1.0
NE2 A:HIS219 4.7 4.4 1.0
ND1 A:HIS219 4.8 2.9 1.0
CO A:CO401 4.9 10.2 1.0
CA A:ASP286 4.9 5.8 1.0
ND2 A:ASN214 5.0 10.2 1.0

Cobalt binding site 2 out of 4 in 1qt1

Go back to Cobalt Binding Sites List in 1qt1
Cobalt binding site 2 out of 4 in the Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co401

b:10.2
occ:1.00
 OD2 A:ASP254 2.0 9.4 1.0
OD1 A:ASP256 2.2 7.4 1.0
OE2 A:GLU216 2.2 7.5 1.0
O A:HOH1635 2.4 45.0 1.0
NE2 A:HIS219 2.5 4.4 1.0
CG A:ASP254 2.7 10.0 1.0
OD1 A:ASP254 2.8 13.0 1.0
CG A:ASP256 3.1 8.3 1.0
CD A:GLU216 3.2 7.0 1.0
OD2 A:ASP256 3.2 13.3 1.0
CD2 A:HIS219 3.3 2.0 1.0
O A:HOH1275 3.3 58.8 1.0
OE1 A:GLU216 3.3 3.4 1.0
CE1 A:HIS219 3.5 4.6 1.0
ND2 A:ASN246 4.1 5.2 1.0
CB A:ASP254 4.2 5.9 1.0
CB A:ASP256 4.5 4.6 1.0
CG A:HIS219 4.5 4.0 1.0
O A:HOH1018 4.5 7.6 1.0
CG A:GLU216 4.5 4.5 1.0
ND1 A:HIS219 4.6 2.9 1.0
OD2 A:ASP286 4.7 12.3 1.0
NZ A:LYS182 4.9 5.5 1.0
CO A:CO400 4.9 16.1 1.0
CE A:LYS182 5.0 2.1 1.0
CA A:ASP256 5.0 4.0 1.0

Cobalt binding site 3 out of 4 in 1qt1

Go back to Cobalt Binding Sites List in 1qt1
Cobalt binding site 3 out of 4 in the Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co900

b:18.0
occ:1.00
 OD2 B:ASP744 1.9 9.3 1.0
OE1 B:GLU716 2.0 5.9 1.0
OD2 B:ASP786 2.0 10.6 1.0
OE2 B:GLU680 2.1 15.6 1.0
CD B:GLU680 2.9 9.5 1.0
CG B:ASP786 3.0 8.1 1.0
CG B:ASP744 3.1 12.3 1.0
OE1 B:GLU680 3.1 10.6 1.0
CD B:GLU716 3.2 7.5 1.0
CB B:ASP786 3.5 5.1 1.0
O B:HOH1410 3.5 17.1 1.0
CB B:ASP744 3.6 7.9 1.0
CG B:GLU716 3.8 7.6 1.0
O B:HOH1636 3.9 48.3 1.0
CB B:GLU716 3.9 2.7 1.0
O B:HOH1407 4.1 34.3 1.0
OD1 B:ASP744 4.1 8.8 1.0
OD1 B:ASP786 4.1 8.7 1.0
OE2 B:GLU716 4.1 9.4 1.0
CG B:GLU680 4.2 6.2 1.0
O B:HOH1235 4.3 36.0 1.0
CE1 B:HIS719 4.3 5.4 1.0
NE2 B:HIS719 4.8 6.3 1.0
OD1 B:ASN714 4.8 11.6 1.0
CO B:CO901 4.9 11.0 1.0
ND1 B:HIS719 4.9 4.4 1.0
O B:HOH1627 5.0 42.5 1.0
CA B:ASP786 5.0 6.0 1.0

Cobalt binding site 4 out of 4 in 1qt1

Go back to Cobalt Binding Sites List in 1qt1
Cobalt binding site 4 out of 4 in the Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co901

b:11.0
occ:1.00
 OD2 B:ASP754 2.1 10.5 1.0
OD1 B:ASP756 2.1 10.8 1.0
OE2 B:GLU716 2.2 9.4 1.0
O B:HOH1636 2.2 48.3 1.0
NE2 B:HIS719 2.6 6.3 1.0
CG B:ASP754 2.8 11.1 1.0
OD1 B:ASP754 2.8 16.1 1.0
CG B:ASP756 3.0 11.9 1.0
CD B:GLU716 3.1 7.5 1.0
OD2 B:ASP756 3.2 14.8 1.0
CD2 B:HIS719 3.3 2.1 1.0
OE1 B:GLU716 3.3 5.9 1.0
O B:HOH1627 3.4 42.5 1.0
CE1 B:HIS719 3.6 5.4 1.0
ND2 B:ASN746 4.0 3.8 1.0
O B:HOH1015 4.2 13.7 1.0
CB B:ASP754 4.2 5.2 1.0
CB B:ASP756 4.4 6.7 1.0
CG B:GLU716 4.5 7.6 1.0
CG B:HIS719 4.5 3.7 1.0
ND1 B:HIS719 4.6 4.4 1.0
OD2 B:ASP786 4.8 10.6 1.0
CO B:CO900 4.9 18.0 1.0
CA B:ASP756 4.9 5.9 1.0
NZ B:LYS682 4.9 2.0 1.0
O B:ASP786 5.0 6.5 1.0

Reference:

X.Zhu, M.Teng, L.Niu, C.Xu, Y.Wang. Structure of Xylose Isomerase From Streptomyces Diastaticus No. 7 Strain M1033 at 1.85 A Resolution. Acta Crystallogr.,Sect.D V. 56 129 2000.
ISSN: ISSN 0907-4449
PubMed: 10666592
DOI: 10.1107/S0907444999015097
Page generated: Sun Jul 13 17:43:04 2025

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