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Nickel in PDB 9gnr: Cryo-Em Structure of Sporosarcina Pasteurii Urease Inhibited By Nbpto

Enzymatic activity of Cryo-Em Structure of Sporosarcina Pasteurii Urease Inhibited By Nbpto

All present enzymatic activity of Cryo-Em Structure of Sporosarcina Pasteurii Urease Inhibited By Nbpto:
3.5.1.5;

Nickel Binding Sites:

The binding sites of Nickel atom in the Cryo-Em Structure of Sporosarcina Pasteurii Urease Inhibited By Nbpto (pdb code 9gnr). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Cryo-Em Structure of Sporosarcina Pasteurii Urease Inhibited By Nbpto, PDB code: 9gnr:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 9gnr

Go back to Nickel Binding Sites List in 9gnr
Nickel binding site 1 out of 2 in the Cryo-Em Structure of Sporosarcina Pasteurii Urease Inhibited By Nbpto


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Cryo-Em Structure of Sporosarcina Pasteurii Urease Inhibited By Nbpto within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni601

b:102.3
occ:1.00
OQ1 C:KCX220 2.0 60.6 1.0
NE2 C:HIS275 2.0 54.2 1.0
O1 C:2PA603 2.0 66.8 1.0
ND1 C:HIS249 2.0 59.3 1.0
O3 C:2PA603 2.0 74.4 1.0
P2 C:2PA603 2.3 53.7 1.0
CE1 C:HIS249 2.7 62.6 1.0
CE1 C:HIS275 2.8 59.8 1.0
CX C:KCX220 2.9 53.5 1.0
CD2 C:HIS275 3.0 56.3 1.0
CG C:HIS249 3.2 52.7 1.0
OQ2 C:KCX220 3.2 68.6 1.0
NI C:NI602 3.5 98.9 1.0
N5 C:2PA603 3.6 51.7 1.0
NE2 C:HIS222 3.7 54.6 1.0
N4 C:2PA603 3.7 64.6 1.0
CE1 C:HIS137 3.7 62.6 1.0
CD2 C:HIS222 3.8 57.9 1.0
CB C:HIS249 3.8 56.1 1.0
NE2 C:HIS249 3.9 57.3 1.0
ND1 C:HIS275 3.9 57.8 1.0
NE2 C:HIS137 4.1 52.1 1.0
NZ C:KCX220 4.1 55.3 1.0
CG C:HIS275 4.1 58.5 1.0
CD2 C:HIS249 4.2 58.5 1.0
CE C:KCX220 4.5 58.6 1.0
O C:GLY280 4.7 79.0 1.0
CB C:PHE274 4.8 57.9 1.0
CE1 C:HIS222 4.9 53.7 1.0
CA C:HIS249 4.9 56.7 1.0
ND1 C:HIS137 5.0 60.8 1.0

Nickel binding site 2 out of 2 in 9gnr

Go back to Nickel Binding Sites List in 9gnr
Nickel binding site 2 out of 2 in the Cryo-Em Structure of Sporosarcina Pasteurii Urease Inhibited By Nbpto


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Cryo-Em Structure of Sporosarcina Pasteurii Urease Inhibited By Nbpto within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni602

b:98.9
occ:1.00
NE2 C:HIS139 2.0 50.7 1.0
OQ2 C:KCX220 2.0 68.6 1.0
NE2 C:HIS137 2.0 52.1 1.0
N4 C:2PA603 2.0 64.6 1.0
O3 C:2PA603 2.1 74.4 1.0
OD1 C:ASP363 2.1 66.8 1.0
P2 C:2PA603 2.5 53.7 1.0
CE1 C:HIS139 2.8 51.7 1.0
CE1 C:HIS137 2.9 62.6 1.0
CG C:ASP363 2.9 61.7 1.0
CX C:KCX220 3.0 53.5 1.0
CD2 C:HIS137 3.1 56.7 1.0
CD2 C:HIS139 3.1 48.1 1.0
OQ1 C:KCX220 3.3 60.6 1.0
O1 C:2PA603 3.5 66.8 1.0
NI C:NI601 3.5 102.3 1.0
OD2 C:ASP363 3.6 63.1 1.0
N5 C:2PA603 3.7 51.7 1.0
CB C:ASP363 3.8 61.6 1.0
ND1 C:HIS137 4.0 60.8 1.0
ND1 C:HIS139 4.0 46.0 1.0
CG C:HIS137 4.1 59.4 1.0
NZ C:KCX220 4.1 55.3 1.0
CG C:HIS139 4.1 51.1 1.0
CG2 C:THR172 4.3 63.3 1.0
CB C:ALA366 4.3 64.7 1.0
CA C:ASP363 4.4 65.3 1.0
O C:ALA170 4.4 60.6 1.0
O C:ALA366 4.4 79.8 1.0
NE2 C:HIS275 4.6 54.2 1.0
O C:ASP363 4.7 70.9 1.0
C C:ASP363 4.7 66.1 1.0
CD2 C:HIS275 4.8 56.3 1.0

Reference:

L.Mazzei, G.Tria, S.Ciurli, M.Cianci. Exploring the Conformational Space of the Mobile Flap in Sporosarcina Pasteurii Urease By Cryo-Electron Microscopy. Int.J.Biol.Macromol. V. 283 37904 2024.
ISSN: ISSN 0141-8130
PubMed: 39571870
DOI: 10.1016/J.IJBIOMAC.2024.137904
Page generated: Mon Aug 18 22:37:13 2025

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