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Cobalt in PDB 2b3h: Crystal Structure of Human Methionine Aminopeptidase Type I with A Third Cobalt in the Active Site

Enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase Type I with A Third Cobalt in the Active Site

All present enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase Type I with A Third Cobalt in the Active Site:
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Human Methionine Aminopeptidase Type I with A Third Cobalt in the Active Site, PDB code: 2b3h was solved by A.Addlagatta, X.Hu, J.O.Liu, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.290, 77.300, 48.340, 90.00, 91.03, 90.00
R / Rfree (%) 9.8 / 13.1

Other elements in 2b3h:

The structure of Crystal Structure of Human Methionine Aminopeptidase Type I with A Third Cobalt in the Active Site also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Human Methionine Aminopeptidase Type I with A Third Cobalt in the Active Site (pdb code 2b3h). 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 Human Methionine Aminopeptidase Type I with A Third Cobalt in the Active Site, PDB code: 2b3h:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 2b3h

Go back to Cobalt Binding Sites List in 2b3h
Cobalt binding site 1 out of 4 in the Crystal Structure of Human Methionine Aminopeptidase Type I with A Third Cobalt 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 Crystal Structure of Human Methionine Aminopeptidase Type I with A Third Cobalt in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co401

b:8.8
occ:1.00
 O A:HOH510 2.0 9.1 1.0
OE2 A:GLU367 2.0 8.8 1.0
NE2 A:HIS303 2.0 8.2 1.0
OD2 A:ASP240 2.1 8.1 1.0
OE1 A:GLU336 2.2 9.2 1.0
CD A:GLU367 3.0 7.4 1.0
CG A:ASP240 3.0 7.9 1.0
CE1 A:HIS303 3.0 8.8 1.0
CD2 A:HIS303 3.1 9.0 1.0
CD A:GLU336 3.1 9.3 1.0
CO A:CO402 3.2 7.7 1.0
CL A:CL406 3.3 46.3 0.5
OE1 A:GLU367 3.3 8.0 1.0
OE2 A:GLU336 3.4 13.7 1.0
OD1 A:ASP240 3.4 7.7 1.0
OG1 A:THR334 3.7 9.6 1.0
O A:HOH937 3.8 8.5 0.4
CG2 A:THR334 3.9 9.4 1.0
CB A:THR334 4.1 9.3 1.0
O A:HOH933 4.2 20.7 0.4
ND1 A:HIS303 4.2 9.9 1.0
O A:HOH505 4.2 10.0 1.0
CB A:ASP240 4.2 8.0 1.0
CG A:HIS303 4.2 9.2 1.0
CG A:GLU367 4.3 7.8 1.0
CG A:GLU336 4.4 9.5 1.0
NE2 A:HIS310 4.8 12.6 1.0
CB A:GLU336 4.8 8.5 1.0
O A:HOH935 4.9 19.6 0.5
CD2 A:HIS310 5.0 13.9 1.0
OD2 A:ASP229 5.0 14.5 1.0

Cobalt binding site 2 out of 4 in 2b3h

Go back to Cobalt Binding Sites List in 2b3h
Cobalt binding site 2 out of 4 in the Crystal Structure of Human Methionine Aminopeptidase Type I with A Third Cobalt 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 Crystal Structure of Human Methionine Aminopeptidase Type I with A Third Cobalt in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co402

b:7.7
occ:1.00
 OD1 A:ASP240 2.0 7.7 1.0
O A:HOH510 2.0 9.1 1.0
OD1 A:ASP229 2.1 11.3 1.0
OE1 A:GLU367 2.1 8.0 1.0
O A:HOH505 2.2 10.0 1.0
OD2 A:ASP229 2.4 14.5 1.0
CG A:ASP229 2.6 9.5 1.0
CG A:ASP240 2.9 7.9 1.0
CD A:GLU367 3.0 7.4 1.0
CO A:CO401 3.2 8.8 1.0
OD2 A:ASP240 3.2 8.1 1.0
OE2 A:GLU367 3.3 8.8 1.0
CL A:CL406 3.6 46.3 0.5
O A:HOH937 3.9 8.5 0.4
OG1 A:THR231 4.0 9.8 1.0
CB A:ASP229 4.2 7.7 1.0
ND2 A:ASN242 4.2 8.3 1.0
O A:HOH936 4.2 13.9 0.5
OE2 A:GLU336 4.3 13.7 1.0
CB A:ASP240 4.3 8.0 1.0
O A:HOH688 4.4 16.7 1.0
CG A:GLU367 4.4 7.8 1.0
O A:LEU241 4.4 6.9 1.0
O A:ILE230 4.4 7.9 1.0
O A:HOH935 4.5 19.6 0.5
N A:LEU241 4.5 7.3 1.0
OE1 A:GLU336 4.6 9.2 1.0
O A:HOH739 4.6 11.6 1.0
C A:LEU241 4.7 6.4 1.0
CD A:GLU336 4.7 9.3 1.0
C A:ASP240 4.8 7.8 1.0
CA A:ASP229 4.9 6.8 1.0
CA A:ASP240 4.9 7.9 1.0
O3 A:GOL471 4.9 38.3 1.0
CB A:ASN242 4.9 7.2 1.0
N A:ILE230 4.9 7.2 1.0
CB A:GLU367 4.9 7.3 1.0
CA A:LEU241 5.0 7.2 1.0

Cobalt binding site 3 out of 4 in 2b3h

Go back to Cobalt Binding Sites List in 2b3h
Cobalt binding site 3 out of 4 in the Crystal Structure of Human Methionine Aminopeptidase Type I with A Third Cobalt 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 Crystal Structure of Human Methionine Aminopeptidase Type I with A Third Cobalt in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co403

b:10.7
occ:0.50
 CO A:CO404 1.4 16.7 0.2
O1 A:GOL471 2.1 23.1 1.0
O3 A:GOL471 2.1 38.3 1.0
O A:HOH935 2.1 19.6 0.5
NE2 A:HIS212 2.1 14.2 1.0
O A:HOH934 2.2 19.1 0.5
O A:HOH936 2.2 13.9 0.5
CL A:CL406 2.3 46.3 0.5
O A:HOH937 2.3 8.5 0.4
CD2 A:HIS212 3.1 11.6 1.0
O A:HOH933 3.1 20.7 0.4
CE1 A:HIS212 3.2 13.6 1.0
C1 A:GOL471 3.3 27.5 1.0
C3 A:GOL471 3.3 27.2 1.0
C2 A:GOL471 3.8 20.5 1.0
O A:HOH510 3.9 9.1 1.0
NE2 A:HIS310 4.1 12.6 1.0
O A:HOH726 4.2 35.9 1.0
O A:HOH938 4.2 53.0 1.0
CG A:HIS212 4.3 9.3 1.0
ND1 A:HIS212 4.3 10.3 1.0
O A:HOH505 4.4 10.0 1.0
O A:HOH939 4.4 21.7 0.4
O A:HOH739 4.5 11.6 1.0
OD2 A:ASP229 4.6 14.5 1.0
CE1 A:HIS310 4.7 13.6 1.0
O2 A:GOL471 4.9 37.9 1.0
OE2 A:GLU336 4.9 13.7 1.0

Cobalt binding site 4 out of 4 in 2b3h

Go back to Cobalt Binding Sites List in 2b3h
Cobalt binding site 4 out of 4 in the Crystal Structure of Human Methionine Aminopeptidase Type I with A Third Cobalt 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 Crystal Structure of Human Methionine Aminopeptidase Type I with A Third Cobalt in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co404

b:16.7
occ:0.20
 O A:HOH934 1.3 19.1 0.5
CO A:CO403 1.4 10.7 0.5
O A:HOH935 1.9 19.6 0.5
NE2 A:HIS212 2.0 14.2 1.0
O A:HOH933 2.3 20.7 0.4
CE1 A:HIS212 2.7 13.6 1.0
CL A:CL406 3.0 46.3 0.5
O1 A:GOL471 3.1 23.1 1.0
O A:HOH936 3.2 13.9 0.5
O A:HOH937 3.3 8.5 0.4
CD2 A:HIS212 3.3 11.6 1.0
O A:HOH938 3.4 53.0 1.0
O A:HOH939 3.4 21.7 0.4
O3 A:GOL471 3.5 38.3 1.0
O A:HOH869 3.8 47.3 0.8
ND1 A:HIS212 4.0 10.3 1.0
CG A:HIS212 4.3 9.3 1.0
O A:HOH510 4.3 9.1 1.0
C1 A:GOL471 4.3 27.5 1.0
O A:HOH726 4.3 35.9 1.0
OE2 A:GLU336 4.4 13.7 1.0
O A:HOH739 4.5 11.6 1.0
O A:HOH721 4.5 45.1 1.0
NE2 A:HIS310 4.5 12.6 1.0
C3 A:GOL471 4.8 27.2 1.0
CD1 A:TYR300 4.8 12.5 1.0

Reference:

A.Addlagatta, X.Hu, J.O.Liu, B.W.Matthews. Structural Basis For the Functional Differences Between Type I and Type II Human Methionine Aminopeptidases(,). Biochemistry V. 44 14741 2005.
ISSN: ISSN 0006-2960
PubMed: 16274222
DOI: 10.1021/BI051691K
Page generated: Tue Jul 30 14:56:31 2024

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