Nickel in PDB 9it2: Cryo-Em Structure of Urease From Ureaplasma Parvum

All present enzymatic activity of Cryo-Em Structure of Urease From Ureaplasma Parvum:
3.5.1.5;

The binding sites of Nickel atom in the Cryo-Em Structure of Urease From Ureaplasma Parvum (pdb code 9it2). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Cryo-Em Structure of Urease From Ureaplasma Parvum, PDB code: 9it2:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the Cryo-Em Structure of Urease From Ureaplasma Parvum


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 Urease From Ureaplasma Parvum within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni602 b:28.7 occ:1.00 NE2 C:HIS278 2.0 24.7 1.0 ND1 C:HIS252 2.0 24.7 1.0 OQ2 C:KCX223 2.0 22.5 1.0 S2 C:BME601 2.6 26.3 1.0 CE1 C:HIS252 2.8 24.7 1.0 CD2 C:HIS278 2.9 24.7 1.0 O1 C:BME601 2.9 26.3 1.0 CX C:KCX223 3.0 22.5 1.0 CE1 C:HIS278 3.0 24.7 1.0 CG C:HIS252 3.1 24.7 1.0 OQ1 C:KCX223 3.3 22.5 1.0 NE2 C:HIS225 3.5 23.1 1.0 CE1 C:HIS141 3.6 22.0 1.0 CB C:HIS252 3.7 24.7 1.0 NI C:NI603 3.7 35.0 1.0 C1 C:BME601 3.8 26.3 1.0 C2 C:BME601 3.9 26.3 1.0 NE2 C:HIS252 4.0 24.7 1.0 CD2 C:HIS225 4.0 23.1 1.0 NE2 C:HIS141 4.0 22.0 1.0 CG C:HIS278 4.1 24.7 1.0 ND1 C:HIS278 4.1 24.7 1.0 OD2 C:ASP366 4.1 23.9 1.0 CD2 C:HIS252 4.2 24.7 1.0 NZ C:KCX223 4.2 22.5 1.0 CE1 C:HIS225 4.5 23.1 1.0 CE C:KCX223 4.6 22.5 1.0 CA C:HIS252 4.7 24.7 1.0 ND1 C:HIS141 4.8 22.0 1.0 CB C:TYR277 4.8 23.3 1.0 CG C:ASP366 4.8 23.9 1.0 OD1 C:ASP366 4.9 23.9 1.0 CD2 C:TYR277 5.0 23.3 1.0

Nickel binding site 2 out of 6 in the Cryo-Em Structure of Urease From Ureaplasma Parvum


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 Urease From Ureaplasma Parvum within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni603 b:35.0 occ:1.00 NE2 C:HIS141 2.0 22.0 1.0 OD1 C:ASP366 2.0 23.9 1.0 NE2 C:HIS143 2.0 19.2 1.0 OQ1 C:KCX223 2.0 22.5 1.0 S2 C:BME601 2.6 26.3 1.0 CG C:ASP366 2.9 23.9 1.0 CE1 C:HIS143 2.9 19.2 1.0 CE1 C:HIS141 2.9 22.0 1.0 CD2 C:HIS141 3.0 22.0 1.0 CD2 C:HIS143 3.0 19.2 1.0 CX C:KCX223 3.1 22.5 1.0 OD2 C:ASP366 3.2 23.9 1.0 OQ2 C:KCX223 3.5 22.5 1.0 C2 C:BME601 3.6 26.3 1.0 NI C:NI602 3.7 28.7 1.0 CG2 C:THR176 3.7 19.8 1.0 ND1 C:HIS143 4.0 19.2 1.0 ND1 C:HIS141 4.0 22.0 1.0 CG C:HIS141 4.1 22.0 1.0 CG C:HIS143 4.1 19.2 1.0 CB C:ASP366 4.2 23.9 1.0 NZ C:KCX223 4.2 22.5 1.0 O1 C:BME601 4.3 26.3 1.0 CB C:ALA369 4.4 24.8 1.0 CA C:ASP366 4.5 23.9 1.0 O C:ALA174 4.6 20.2 1.0 C1 C:BME601 4.6 26.3 1.0 N C:THR176 4.8 19.8 1.0 NE2 C:HIS225 4.9 23.1 1.0 CB C:THR176 5.0 19.8 1.0

Nickel binding site 3 out of 6 in the Cryo-Em Structure of Urease From Ureaplasma Parvum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Cryo-Em Structure of Urease From Ureaplasma Parvum within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni602 b:28.2 occ:1.00 NE2 F:HIS278 2.0 24.2 1.0 ND1 F:HIS252 2.0 24.6 1.0 OQ2 F:KCX223 2.0 22.2 1.0 S2 F:BME601 2.6 26.9 1.0 CE1 F:HIS252 2.8 24.6 1.0 O1 F:BME601 2.9 26.9 1.0 CD2 F:HIS278 2.9 24.2 1.0 CE1 F:HIS278 3.0 24.2 1.0 CX F:KCX223 3.0 22.2 1.0 CG F:HIS252 3.1 24.6 1.0 OQ1 F:KCX223 3.3 22.2 1.0 NE2 F:HIS225 3.5 22.9 1.0 CE1 F:HIS141 3.6 21.4 1.0 CB F:HIS252 3.6 24.6 1.0 NI F:NI603 3.7 34.1 1.0 C1 F:BME601 3.8 26.9 1.0 C2 F:BME601 3.9 26.9 1.0 CD2 F:HIS225 4.0 22.9 1.0 NE2 F:HIS252 4.0 24.6 1.0 NE2 F:HIS141 4.0 21.4 1.0 OD2 F:ASP366 4.1 24.0 1.0 ND1 F:HIS278 4.1 24.2 1.0 CG F:HIS278 4.1 24.2 1.0 CD2 F:HIS252 4.2 24.6 1.0 NZ F:KCX223 4.2 22.2 1.0 CE1 F:HIS225 4.5 22.9 1.0 CE F:KCX223 4.6 22.2 1.0 CA F:HIS252 4.7 24.6 1.0 ND1 F:HIS141 4.8 21.4 1.0 CG F:ASP366 4.8 24.0 1.0 CB F:TYR277 4.9 22.4 1.0 OD1 F:ASP366 4.9 24.0 1.0

Nickel binding site 4 out of 6 in the Cryo-Em Structure of Urease From Ureaplasma Parvum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Cryo-Em Structure of Urease From Ureaplasma Parvum within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni603 b:34.1 occ:1.00 NE2 F:HIS141 2.0 21.4 1.0 OD1 F:ASP366 2.0 24.0 1.0 NE2 F:HIS143 2.0 19.3 1.0 OQ1 F:KCX223 2.0 22.2 1.0 S2 F:BME601 2.6 26.9 1.0 CG F:ASP366 2.8 24.0 1.0 CE1 F:HIS143 2.9 19.3 1.0 CE1 F:HIS141 2.9 21.4 1.0 CD2 F:HIS141 3.0 21.4 1.0 CD2 F:HIS143 3.0 19.3 1.0 CX F:KCX223 3.1 22.2 1.0 OD2 F:ASP366 3.2 24.0 1.0 OQ2 F:KCX223 3.5 22.2 1.0 C2 F:BME601 3.5 26.9 1.0 CG2 F:THR176 3.7 19.8 1.0 NI F:NI602 3.7 28.2 1.0 ND1 F:HIS143 4.0 19.3 1.0 ND1 F:HIS141 4.0 21.4 1.0 CG F:HIS141 4.1 21.4 1.0 CG F:HIS143 4.1 19.3 1.0 CB F:ASP366 4.1 24.0 1.0 NZ F:KCX223 4.2 22.2 1.0 O1 F:BME601 4.3 26.9 1.0 CB F:ALA369 4.4 24.9 1.0 CA F:ASP366 4.4 24.0 1.0 C1 F:BME601 4.6 26.9 1.0 O F:ALA174 4.7 20.3 1.0 N F:THR176 4.9 19.8 1.0 CB F:THR176 5.0 19.8 1.0

Nickel binding site 5 out of 6 in the Cryo-Em Structure of Urease From Ureaplasma Parvum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Cryo-Em Structure of Urease From Ureaplasma Parvum within 5.0Å range: probe atom residue distance (Å) B Occ I:Ni602 b:28.7 occ:1.00 NE2 I:HIS278 2.0 24.1 1.0 ND1 I:HIS252 2.0 24.1 1.0 OQ2 I:KCX223 2.0 22.3 1.0 S2 I:BME601 2.6 25.9 1.0 CE1 I:HIS252 2.7 24.1 1.0 O1 I:BME601 2.8 25.9 1.0 CD2 I:HIS278 2.9 24.1 1.0 CX I:KCX223 3.0 22.3 1.0 CE1 I:HIS278 3.0 24.1 1.0 CG I:HIS252 3.2 24.1 1.0 OQ1 I:KCX223 3.3 22.3 1.0 NE2 I:HIS225 3.6 22.6 1.0 CE1 I:HIS141 3.6 21.6 1.0 NI I:NI603 3.7 35.5 1.0 C1 I:BME601 3.7 25.9 1.0 CB I:HIS252 3.8 24.1 1.0 C2 I:BME601 3.8 25.9 1.0 NE2 I:HIS252 3.9 24.1 1.0 NE2 I:HIS141 4.0 21.6 1.0 CD2 I:HIS225 4.0 22.6 1.0 OD2 I:ASP366 4.1 23.8 1.0 CG I:HIS278 4.1 24.1 1.0 ND1 I:HIS278 4.1 24.1 1.0 NZ I:KCX223 4.2 22.3 1.0 CD2 I:HIS252 4.2 24.1 1.0 CE1 I:HIS225 4.5 22.6 1.0 CE I:KCX223 4.6 22.3 1.0 CG I:ASP366 4.8 23.8 1.0 CA I:HIS252 4.8 24.1 1.0 ND1 I:HIS141 4.8 21.6 1.0 OD1 I:ASP366 4.9 23.8 1.0 CB I:TYR277 4.9 22.5 1.0

Nickel binding site 6 out of 6 in the Cryo-Em Structure of Urease From Ureaplasma Parvum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Cryo-Em Structure of Urease From Ureaplasma Parvum within 5.0Å range: probe atom residue distance (Å) B Occ I:Ni603 b:35.5 occ:1.00 NE2 I:HIS141 2.0 21.6 1.0 NE2 I:HIS143 2.0 19.2 1.0 OD1 I:ASP366 2.0 23.8 1.0 OQ1 I:KCX223 2.0 22.3 1.0 S2 I:BME601 2.6 25.9 1.0 CG I:ASP366 2.9 23.8 1.0 CE1 I:HIS143 2.9 19.2 1.0 CD2 I:HIS141 2.9 21.6 1.0 CE1 I:HIS141 3.0 21.6 1.0 CD2 I:HIS143 3.0 19.2 1.0 CX I:KCX223 3.1 22.3 1.0 OD2 I:ASP366 3.2 23.8 1.0 OQ2 I:KCX223 3.5 22.3 1.0 C2 I:BME601 3.7 25.9 1.0 NI I:NI602 3.7 28.7 1.0 CG2 I:THR176 3.7 19.8 1.0 ND1 I:HIS143 4.0 19.2 1.0 ND1 I:HIS141 4.0 21.6 1.0 CG I:HIS141 4.1 21.6 1.0 CG I:HIS143 4.1 19.2 1.0 CB I:ASP366 4.1 23.8 1.0 NZ I:KCX223 4.2 22.3 1.0 CB I:ALA369 4.3 24.7 1.0 O1 I:BME601 4.4 25.9 1.0 CA I:ASP366 4.4 23.8 1.0 O I:ALA174 4.5 19.8 1.0 C1 I:BME601 4.7 25.9 1.0 N I:THR176 4.9 19.8 1.0 NE2 I:HIS225 5.0 22.6 1.0 CB I:THR176 5.0 19.8 1.0

H.N.Wu, J.Fujita, Y.Nakura, M.Inoue, K.Suzuki, T.Ekimoto, B.Yin, Y.Fukuda, K.Harada, T.Inoue, M.Ikeguchi, K.Namba, I.Yanagihara. Structural Analysis and Molecular Dynamics Simulations of Urease From Ureaplasma Parvum. J.Mol.Biol. V. 437 69368 2025.
ISSN: ESSN 1089-8638
PubMed: 40752870
DOI: 10.1016/J.JMB.2025.169368