Atomistry » Cobalt » PDB 5vtd-5zt2 » 5yr7
Atomistry »
  Cobalt »
    PDB 5vtd-5zt2 »
      5yr7 »

Cobalt in PDB 5yr7: Human Methionine Aminopeptidase Type 1B (F309L Mutant)

Enzymatic activity of Human Methionine Aminopeptidase Type 1B (F309L Mutant)

All present enzymatic activity of Human Methionine Aminopeptidase Type 1B (F309L Mutant):
3.4.11.18;

Protein crystallography data

The structure of Human Methionine Aminopeptidase Type 1B (F309L Mutant), PDB code: 5yr7 was solved by V.Pillalamarri, T.Arya, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.69 / 2.06
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.414, 77.193, 48.220, 90.00, 92.03, 90.00
R / Rfree (%) 19.6 / 26.6

Other elements in 5yr7:

The structure of Human Methionine Aminopeptidase Type 1B (F309L Mutant) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Human Methionine Aminopeptidase Type 1B (F309L Mutant) (pdb code 5yr7). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Human Methionine Aminopeptidase Type 1B (F309L Mutant), PDB code: 5yr7:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 5yr7

Go back to Cobalt Binding Sites List in 5yr7
Cobalt binding site 1 out of 4 in the Human Methionine Aminopeptidase Type 1B (F309L Mutant)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Human Methionine Aminopeptidase Type 1B (F309L Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co401

b:27.5
occ:1.00
OE1 A:GLU367 2.0 24.5 1.0
OD1 A:ASP240 2.0 22.4 1.0
OD1 A:ASP229 2.2 24.8 1.0
O A:MET406 2.3 22.4 0.5
N A:MET406 2.3 21.6 0.5
OD2 A:ASP229 2.4 22.9 1.0
CG A:ASP229 2.6 21.2 1.0
CA A:MET406 2.9 24.4 0.5
C A:MET406 2.9 24.6 0.5
CG A:ASP240 2.9 24.2 1.0
CD A:GLU367 3.0 25.4 1.0
CO A:CO402 3.1 24.1 1.0
OD2 A:ASP240 3.2 17.0 1.0
OE2 A:GLU367 3.4 26.1 1.0
OXT A:MET406 4.1 25.7 0.5
CB A:ASP229 4.1 23.0 1.0
OG1 A:THR231 4.2 24.9 0.7
CG2 A:THR231 4.2 24.6 0.3
O A:HOH503 4.3 23.6 1.0
ND2 A:ASN242 4.3 26.6 1.0
CG A:GLU367 4.3 24.9 1.0
CB A:MET406 4.3 26.7 0.5
OE2 A:GLU336 4.3 28.6 1.0
CB A:ASP240 4.4 24.6 1.0
OE1 A:GLU336 4.4 22.8 1.0
O A:LEU241 4.4 22.6 1.0
O A:HOH545 4.5 14.0 0.5
N A:LEU241 4.5 25.6 1.0
CD A:GLU336 4.7 24.0 1.0
O A:ILE230 4.7 26.0 1.0
C A:LEU241 4.7 24.5 1.0
CB A:GLU367 4.7 24.3 1.0
C A:ASP240 4.8 26.0 1.0
CB A:ASN242 4.8 25.5 1.0
CA A:ASP240 4.8 25.4 1.0
CA A:ASP229 4.9 20.6 1.0
CA A:LEU241 4.9 25.8 1.0

Cobalt binding site 2 out of 4 in 5yr7

Go back to Cobalt Binding Sites List in 5yr7
Cobalt binding site 2 out of 4 in the Human Methionine Aminopeptidase Type 1B (F309L Mutant)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Human Methionine Aminopeptidase Type 1B (F309L Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co402

b:24.1
occ:1.00
O A:MET406 1.8 22.4 0.5
OE1 A:GLU336 1.9 22.8 1.0
OE2 A:GLU367 2.0 26.1 1.0
OD2 A:ASP240 2.1 17.0 1.0
NE2 A:HIS303 2.2 27.1 1.0
CD A:GLU367 2.8 25.4 1.0
C A:MET406 2.9 24.6 0.5
CD A:GLU336 2.9 24.0 1.0
CG A:ASP240 3.0 24.2 1.0
OE1 A:GLU367 3.1 24.5 1.0
CO A:CO401 3.1 27.5 1.0
CD2 A:HIS303 3.2 28.0 1.0
CE1 A:HIS303 3.2 33.5 1.0
OXT A:MET406 3.3 25.7 0.5
OE2 A:GLU336 3.3 28.6 1.0
OD1 A:ASP240 3.5 22.4 1.0
OG1 A:THR334 3.6 28.6 1.0
CG2 A:THR334 3.9 25.2 1.0
CB A:THR334 4.1 27.9 1.0
CA A:MET406 4.1 24.4 0.5
CG A:GLU367 4.2 24.9 1.0
CG A:GLU336 4.2 24.8 1.0
N A:MET406 4.2 21.6 0.5
CB A:ASP240 4.3 24.6 1.0
ND1 A:HIS303 4.3 29.5 1.0
CG A:HIS303 4.3 29.3 1.0
CB A:GLU336 4.7 26.5 1.0
O A:HOH545 4.8 14.0 0.5
NE2 A:HIS310 4.8 54.0 1.0

Cobalt binding site 3 out of 4 in 5yr7

Go back to Cobalt Binding Sites List in 5yr7
Cobalt binding site 3 out of 4 in the Human Methionine Aminopeptidase Type 1B (F309L Mutant)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Human Methionine Aminopeptidase Type 1B (F309L Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co403

b:47.7
occ:0.50
NE2 A:HIS212 2.2 35.5 1.0
O A:HOH545 2.4 14.0 0.5
O A:HOH561 2.4 23.1 0.5
OXT A:MET406 2.5 25.7 0.5
CE1 A:HIS212 2.9 32.6 1.0
C A:MET406 3.0 24.6 0.5
CD2 A:HIS212 3.3 35.7 1.0
CA A:MET406 3.5 24.4 0.5
CG A:MET406 3.6 27.2 0.5
CB A:MET406 3.6 26.7 0.5
O A:MET406 3.8 22.4 0.5
NE2 A:HIS310 4.0 54.0 1.0
ND1 A:HIS212 4.1 31.1 1.0
OE2 A:GLU336 4.3 28.6 1.0
CG A:HIS212 4.3 31.7 1.0
CE1 A:HIS310 4.5 56.8 1.0
O A:HOH503 4.6 23.6 1.0
N A:MET406 5.0 21.6 0.5

Cobalt binding site 4 out of 4 in 5yr7

Go back to Cobalt Binding Sites List in 5yr7
Cobalt binding site 4 out of 4 in the Human Methionine Aminopeptidase Type 1B (F309L Mutant)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Human Methionine Aminopeptidase Type 1B (F309L Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co404

b:40.8
occ:0.50
O A:HOH564 2.1 21.4 0.5
NE2 A:HIS99 2.2 41.5 1.0
O A:HOH568 2.3 31.9 0.5
CE1 A:HIS99 3.1 41.1 1.0
CD2 A:HIS99 3.2 37.5 1.0
ND1 A:HIS99 4.2 39.3 1.0
CG A:HIS99 4.3 37.4 1.0
O A:HOH559 4.4 35.5 1.0

Reference:

V.Pillalamarri, T.Arya, A.Addlagatta. Differential Inhibition of Sub-Type 1 Methionine Aminopeptidases By Ovalicin To Be Published.
Page generated: Tue Jul 30 18:21:15 2024

Last articles

Cl in 3L6T
Cl in 3L6H
Cl in 3L4P
Cl in 3L5O
Cl in 3L5J
Cl in 3L5K
Cl in 3L5I
Cl in 3L5B
Cl in 3L50
Cl in 3L59
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy