Nickel in PDB 4g7e: Crystal Structure of Pigeon Pea Urease

All present enzymatic activity of Crystal Structure of Pigeon Pea Urease:
3.5.1.5;

The structure of Crystal Structure of Pigeon Pea Urease, PDB code: 4g7e was solved by A.Balasubramanian, K.Ponnuraj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.70 / 2.20
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	176.292, 176.292, 346.438, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 26.8

The structure of Crystal Structure of Pigeon Pea Urease also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Nickel atom in the Crystal Structure of Pigeon Pea Urease (pdb code 4g7e). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Pigeon Pea Urease, PDB code: 4g7e:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of Pigeon Pea Urease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Pigeon Pea Urease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni901 b:40.4 occ:1.00 ND1 A:HIS519 2.1 32.5 1.0 O A:HOH1003 2.1 20.5 1.0 OQ2 A:KCX490 2.1 22.2 1.0 O A:HOH1001 2.2 21.1 1.0 NE2 A:HIS545 2.2 28.3 1.0 CE1 A:HIS519 3.0 31.9 1.0 CE1 A:HIS545 3.1 29.7 1.0 CG A:HIS519 3.1 30.8 1.0 CX A:KCX490 3.2 23.9 1.0 CD2 A:HIS545 3.3 28.8 1.0 O A:HOH1004 3.3 32.8 1.0 O A:GLY550 3.4 30.9 1.0 OQ1 A:KCX490 3.4 20.4 1.0 O A:HOH1002 3.5 23.5 1.0 CB A:HIS519 3.5 29.0 1.0 NE2 A:HIS492 3.6 28.9 1.0 NI A:NI902 3.7 34.1 1.0 CD2 A:HIS492 4.0 28.2 1.0 CE1 A:HIS407 4.1 29.7 1.0 NE2 A:HIS519 4.1 32.0 1.0 CD2 A:HIS519 4.2 32.0 1.0 ND1 A:HIS545 4.3 28.9 1.0 O A:HOH1286 4.3 34.1 1.0 CG A:HIS545 4.4 30.4 1.0 C A:GLY550 4.4 31.4 1.0 NE2 A:HIS407 4.4 30.5 1.0 NZ A:KCX490 4.4 19.2 1.0 OD2 A:ASP633 4.6 30.8 1.0 CE1 A:HIS492 4.7 30.0 1.0 CA A:HIS519 4.8 29.3 1.0 CE A:KCX490 4.8 20.0 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of Pigeon Pea Urease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Pigeon Pea Urease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni902 b:34.1 occ:1.00 NE2 A:HIS409 2.1 28.9 1.0 NE2 A:HIS407 2.1 30.5 1.0 OQ1 A:KCX490 2.1 20.4 1.0 OD1 A:ASP633 2.2 33.7 1.0 O A:HOH1003 2.4 20.5 1.0 O A:HOH1002 2.4 23.5 1.0 CE1 A:HIS409 2.8 26.9 1.0 CE1 A:HIS407 3.0 29.7 1.0 CG A:ASP633 3.1 29.6 1.0 CD2 A:HIS407 3.1 28.1 1.0 CX A:KCX490 3.2 23.9 1.0 CD2 A:HIS409 3.3 26.3 1.0 O A:HOH1001 3.3 21.1 1.0 OD2 A:ASP633 3.3 30.8 1.0 OQ2 A:KCX490 3.4 22.2 1.0 NI A:NI901 3.7 40.4 1.0 ND1 A:HIS409 4.0 27.2 1.0 O A:HOH1004 4.1 32.8 1.0 ND1 A:HIS407 4.2 28.7 1.0 O A:ALA636 4.2 30.7 1.0 CG A:HIS407 4.2 28.3 1.0 CG2 A:THR442 4.3 25.0 1.0 CG A:HIS409 4.3 27.3 1.0 NZ A:KCX490 4.3 19.2 1.0 CB A:ALA636 4.4 30.4 1.0 CB A:ASP633 4.5 28.4 1.0 O A:ALA440 4.5 27.6 1.0 CA A:ASP633 4.7 28.6 1.0 NE2 A:HIS545 4.9 28.3 1.0 CD2 A:HIS545 5.0 28.8 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of Pigeon Pea Urease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Pigeon Pea Urease within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni901 b:33.0 occ:1.00 NE2 B:HIS409 2.1 28.8 1.0 OQ2 B:KCX490 2.1 21.8 1.0 OD1 B:ASP633 2.1 33.8 1.0 NE2 B:HIS407 2.1 30.8 1.0 O B:HOH1001 2.2 29.7 1.0 O B:HOH1002 2.3 35.6 1.0 CE1 B:HIS409 2.9 27.5 1.0 CE1 B:HIS407 3.1 29.2 1.0 CG B:ASP633 3.1 30.1 1.0 CD2 B:HIS407 3.1 28.3 1.0 CX B:KCX490 3.1 21.9 1.0 CD2 B:HIS409 3.2 25.0 1.0 OD2 B:ASP633 3.4 31.3 1.0 OQ1 B:KCX490 3.4 20.0 1.0 O B:HOH1004 3.5 18.1 1.0 O B:HOH1003 3.5 22.1 1.0 NI B:NI902 3.7 37.2 1.0 ND1 B:HIS409 4.1 26.5 1.0 ND1 B:HIS407 4.2 28.7 1.0 NZ B:KCX490 4.2 19.8 1.0 CG2 B:THR442 4.2 24.4 1.0 CG B:HIS407 4.2 28.7 1.0 CG B:HIS409 4.3 26.7 1.0 O B:ALA636 4.3 30.4 1.0 CB B:ALA636 4.4 30.4 1.0 CB B:ASP633 4.4 28.2 1.0 CA B:ASP633 4.7 28.5 1.0 O B:ALA440 4.7 27.2 1.0 N B:THR442 4.9 25.2 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of Pigeon Pea Urease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Pigeon Pea Urease within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni902 b:37.2 occ:1.00 OQ1 B:KCX490 1.9 20.0 1.0 NE2 B:HIS545 2.1 28.4 1.0 O B:HOH1004 2.2 18.1 1.0 ND1 B:HIS519 2.2 32.3 1.0 O B:HOH1001 2.2 29.7 1.0 CX B:KCX490 3.0 21.9 1.0 CE1 B:HIS519 3.1 31.1 1.0 CD2 B:HIS545 3.1 29.0 1.0 CE1 B:HIS545 3.1 29.0 1.0 CG B:HIS519 3.1 30.6 1.0 OQ2 B:KCX490 3.2 21.8 1.0 O B:GLY550 3.3 30.2 1.0 CB B:HIS519 3.5 29.0 1.0 O B:HOH1003 3.5 22.1 1.0 NI B:NI901 3.7 33.0 1.0 NE2 B:HIS492 3.7 28.6 1.0 O B:HOH1002 3.9 35.6 1.0 CE1 B:HIS407 4.0 29.2 1.0 CD2 B:HIS492 4.1 28.2 1.0 NE2 B:HIS519 4.2 31.8 1.0 NZ B:KCX490 4.2 19.8 1.0 ND1 B:HIS545 4.2 28.9 1.0 CD2 B:HIS519 4.2 32.0 1.0 CG B:HIS545 4.2 30.0 1.0 NE2 B:HIS407 4.3 30.8 1.0 C B:GLY550 4.3 30.7 1.0 OD2 B:ASP633 4.4 31.3 1.0 CA B:HIS519 4.7 29.3 1.0 CE1 B:HIS492 4.8 29.7 1.0 CE B:KCX490 4.8 18.8 1.0 CA B:GLY551 4.9 30.9 1.0 CB B:TYR544 5.0 29.1 1.0 OD1 B:ASP633 5.0 33.8 1.0 CD2 B:TYR544 5.0 27.1 1.0

A.Balasubramanian, V.Durairajpandian, S.Elumalai, N.Mathivanan, A.K.Munirajan, K.Ponnuraj. Structural and Functional Studies on Urease From Pigeon Pea (Cajanus Cajan) Int.J.Biol.Macromol. V. 58C 301 2013.
ISSN: ISSN 0141-8130
PubMed: 23624166
DOI: 10.1016/J.IJBIOMAC.2013.04.055