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Cobalt in PDB 5yr4: Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with TNP470

Enzymatic activity of Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with TNP470

All present enzymatic activity of Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with TNP470:
3.4.11.18;

Protein crystallography data

The structure of Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with TNP470, PDB code: 5yr4 was solved by T.Arya, V.Pillalamarri, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.58 / 1.82
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.210, 77.241, 47.174, 90.00, 92.03, 90.00
R / Rfree (%) 17.3 / 22.7

Other elements in 5yr4:

The structure of Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with TNP470 also contains other interesting chemical elements:

Potassium (K) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with TNP470 (pdb code 5yr4). 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 (F309M Mutant) in Complex with TNP470, PDB code: 5yr4:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 5yr4

Go back to Cobalt Binding Sites List in 5yr4
Cobalt binding site 1 out of 4 in the Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with TNP470


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 (F309M Mutant) in Complex with TNP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co401

b:22.6
occ:1.00
 O A:HOH475 2.0 27.9 1.0
OD1 A:ASP240 2.0 21.0 1.0
OE1 A:GLU367 2.1 21.6 1.0
O A:HOH446 2.1 23.3 1.0
OD2 A:ASP229 2.2 22.3 1.0
OD1 A:ASP229 2.3 22.5 1.0
CG A:ASP229 2.6 20.1 1.0
CG A:ASP240 2.8 23.1 1.0
CD A:GLU367 3.0 23.1 1.0
OD2 A:ASP240 3.0 20.3 1.0
CO A:CO402 3.1 24.9 1.0
OE2 A:GLU367 3.3 22.1 1.0
O A:HOH522 4.0 25.4 0.5
OG1 A:THR231 4.1 27.3 0.7
ND2 A:ASN242 4.1 20.9 1.0
CB A:ASP229 4.1 18.8 1.0
OE2 A:GLU336 4.1 26.3 1.0
CG2 A:THR231 4.2 25.0 0.3
O A:HOH574 4.2 25.0 0.2
O A:HOH544 4.2 10.5 0.3
CB A:ASP240 4.2 23.9 1.0
O11 A:TN4410 4.3 26.3 0.8
O A:HOH424 4.3 24.1 1.0
O A:HOH573 4.3 33.2 0.2
CG A:GLU367 4.4 21.0 1.0
OE1 A:GLU336 4.5 22.6 1.0
O A:LEU241 4.5 19.7 1.0
N A:LEU241 4.5 21.8 1.0
CD A:GLU336 4.7 23.4 1.0
C A:LEU241 4.7 20.3 1.0
C A:ASP240 4.8 22.0 1.0
O A:ILE230 4.8 19.8 1.0
CA A:ASP240 4.8 21.7 1.0
O A:HOH494 4.9 20.7 0.6
CB A:GLU367 4.9 19.7 1.0
CB A:ASN242 5.0 20.2 1.0
CA A:LEU241 5.0 22.5 1.0

Cobalt binding site 2 out of 4 in 5yr4

Go back to Cobalt Binding Sites List in 5yr4
Cobalt binding site 2 out of 4 in the Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with TNP470


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 (F309M Mutant) in Complex with TNP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co402

b:24.9
occ:1.00
 O A:HOH475 2.0 27.9 1.0
OD2 A:ASP240 2.0 20.3 1.0
OE2 A:GLU367 2.1 22.1 1.0
NE2 A:HIS303 2.1 23.4 1.0
OE1 A:GLU336 2.1 22.6 1.0
CD A:GLU367 3.0 23.1 1.0
CG A:ASP240 3.0 23.1 1.0
CE1 A:HIS303 3.0 25.8 1.0
CD A:GLU336 3.1 23.4 1.0
CO A:CO401 3.1 22.6 1.0
CD2 A:HIS303 3.1 25.1 1.0
OE1 A:GLU367 3.3 21.6 1.0
OE2 A:GLU336 3.4 26.3 1.0
O11 A:TN4410 3.4 26.3 0.8
OD1 A:ASP240 3.5 21.0 1.0
OG1 A:THR334 3.6 22.8 1.0
CG2 A:THR334 3.9 21.4 1.0
O A:HOH522 4.0 25.4 0.5
CB A:THR334 4.0 22.6 1.0
O A:HOH573 4.2 33.2 0.2
O A:HOH446 4.2 23.3 1.0
CB A:ASP240 4.2 23.9 1.0
ND1 A:HIS303 4.2 23.1 1.0
CG A:HIS303 4.2 24.8 1.0
CG A:GLU367 4.3 21.0 1.0
CG A:GLU336 4.4 22.3 1.0
C5 A:TN4410 4.7 34.4 0.8
CE1 A:HIS310 4.7 23.8 0.2
C1 A:TN4410 4.8 32.5 0.8
CB A:GLU336 4.9 23.1 1.0
C6 A:TN4410 4.9 33.7 0.8
OD2 A:ASP229 4.9 22.3 1.0
ND1 A:HIS310 5.0 24.9 0.2

Cobalt binding site 3 out of 4 in 5yr4

Go back to Cobalt Binding Sites List in 5yr4
Cobalt binding site 3 out of 4 in the Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with TNP470


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 (F309M Mutant) in Complex with TNP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co403

b:23.1
occ:0.20
 C11 A:TN4410 0.7 29.6 0.8
C1 A:TN4410 0.8 32.5 0.8
C6 A:TN4410 1.8 33.7 0.8
O A:HOH573 1.8 33.2 0.2
O11 A:TN4410 2.0 26.3 0.8
NE2 A:HIS212 2.0 26.7 1.0
C2 A:TN4410 2.1 32.3 0.8
O A:HOH575 2.3 30.1 0.2
O A:HOH574 2.3 25.0 0.2
CE1 A:HIS212 2.9 26.7 1.0
C21 A:TN4410 3.1 38.1 0.8
C5 A:TN4410 3.1 34.4 0.8
CD2 A:HIS212 3.2 25.5 1.0
C3 A:TN4410 3.3 32.2 0.8
C22 A:TN4410 3.3 39.7 0.8
C4 A:TN4410 3.7 33.3 0.8
C2A A:TN4410 3.7 35.6 0.8
O A:HOH475 3.9 27.9 1.0
O41 A:TN4410 4.0 34.6 0.8
O2A A:TN4410 4.0 38.6 0.8
O A:HOH544 4.0 10.5 0.3
ND1 A:HIS212 4.0 25.4 1.0
C24 A:TN4410 4.1 37.1 0.8
CG A:HIS212 4.2 23.9 1.0
O A:HOH522 4.3 25.4 0.5
C23 A:TN4410 4.3 37.0 0.8
CE1 A:HIS310 4.4 23.8 0.2
O A:HOH446 4.4 23.3 1.0
O31 A:TN4410 4.4 31.1 0.8
O A:HOH572 4.5 20.7 0.2
O A:HOH424 4.5 24.1 1.0
OE2 A:GLU336 4.7 26.3 1.0
O A:HOH571 4.7 27.6 0.6
C25 A:TN4410 4.8 31.1 0.8
NE2 A:HIS310 4.8 24.8 0.2
C2C A:TN4410 5.0 30.8 0.8

Cobalt binding site 4 out of 4 in 5yr4

Go back to Cobalt Binding Sites List in 5yr4
Cobalt binding site 4 out of 4 in the Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with TNP470


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 (F309M Mutant) in Complex with TNP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co404

b:51.9
occ:0.40
 NE2 A:HIS310 2.1 40.5 0.8
O A:HOH576 2.3 13.7 0.2
OH A:TYR195 2.4 44.5 1.0
CD2 A:HIS310 3.1 36.5 0.8
O A:HOH577 3.1 16.3 0.2
CE1 A:HIS310 3.2 41.1 0.8
CZ A:TYR195 3.3 43.0 1.0
OE1 A:GLU128 3.5 65.1 1.0
CE2 A:TYR195 3.6 39.5 1.0
CE1 A:TYR196 4.0 49.7 1.0
CG A:HIS310 4.2 37.3 0.8
ND1 A:HIS310 4.2 42.5 0.8
CD A:GLU128 4.3 69.7 1.0
CZ A:TYR196 4.4 55.2 1.0
CD1 A:TYR196 4.5 44.1 1.0
OH A:TYR196 4.5 68.7 1.0
CE1 A:TYR195 4.5 39.7 1.0
O2A A:TN4410 4.6 38.6 0.8
CD2 A:HIS310 4.6 23.9 0.2
OE2 A:GLU128 4.7 67.6 1.0
CD2 A:TYR195 4.9 34.0 1.0

Reference:

V.Pillalamarri, T.Arya, N.Haque, S.C.Bala, A.K.Marapaka, A.Addlagatta. Discovery of Natural Product Ovalicin Sensitive Type 1 Methionine Aminopeptidases: Molecular and Structural Basis. Biochem. J. V. 476 991 2019.
ISSN: ESSN 1470-8728
PubMed: 30837307
DOI: 10.1042/BCJ20180874
Page generated: Tue Jul 30 18:21:05 2024

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