Zinc in PDB 2zet: Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin

The structure of Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin, PDB code: 2zet was solved by M.Kukimoto-Niino, A.Sakamoto, E.Kanno, K.Hanawa-Suetsugu, T.Terada, M.Shirouzu, M.Fukuda, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.28 / 3.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	82.208, 82.208, 325.484, 90.00, 90.00, 90.00
R / Rfree (%)	24.7 / 29.6

The structure of Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin (pdb code 2zet). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin, PDB code: 2zet:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:64.2 occ:1.00 SG C:CYS84 2.3 87.0 1.0 SG C:CYS107 2.4 67.4 1.0 SG C:CYS104 2.4 42.9 1.0 SG C:CYS81 2.5 65.8 1.0 CB C:CYS81 2.9 75.8 1.0 CB C:CYS84 3.1 75.6 1.0 N C:CYS84 3.3 80.0 1.0 CB C:CYS107 3.5 62.6 1.0 CA C:CYS84 3.7 79.7 1.0 CB C:CYS104 3.7 43.9 1.0 NH2 C:ARG50 3.8 94.4 1.0 CB C:GLU83 4.2 86.8 1.0 N C:CYS104 4.3 52.1 1.0 C C:CYS84 4.3 79.1 1.0 C C:GLU83 4.4 80.7 1.0 CA C:CYS81 4.4 71.7 1.0 NH1 C:ARG50 4.5 0.4 1.0 N C:SER85 4.5 80.5 1.0 CA C:CYS104 4.6 56.3 1.0 CZ C:ARG50 4.6 0.5 1.0 CA C:GLU83 4.7 80.5 1.0 CA C:CYS107 4.7 63.3 1.0 N C:CYS107 4.8 60.2 1.0 N C:GLU83 4.8 81.2 1.0 CG C:GLU83 4.8 91.9 1.0 C C:CYS81 4.9 75.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:61.2 occ:1.00 SG C:CYS67 2.3 65.5 1.0 SG C:CYS64 2.4 50.1 1.0 SG C:CYS92 2.5 64.4 1.0 SG C:CYS89 2.5 55.9 1.0 CB C:CYS64 3.1 52.8 1.0 CB C:CYS67 3.3 57.7 1.0 CB C:CYS92 3.4 60.0 1.0 CB C:CYS89 3.5 52.2 1.0 N C:CYS67 3.6 60.5 1.0 N C:CYS89 3.8 54.8 1.0 CA C:CYS67 4.0 55.6 1.0 CA C:CYS89 4.2 53.3 1.0 CB C:ARG66 4.5 74.4 1.0 N C:CYS92 4.5 54.9 1.0 CA C:CYS92 4.6 56.7 1.0 CA C:CYS64 4.6 59.5 1.0 C C:ARG66 4.7 61.3 1.0 C C:CYS67 4.8 53.6 1.0 C C:CYS89 4.8 55.8 1.0 O C:CYS89 4.9 50.0 1.0 N C:LEU68 4.9 55.0 1.0 C C:VAL88 4.9 58.7 1.0 N C:ARG66 4.9 63.9 1.0 CA C:ARG66 4.9 61.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:70.3 occ:1.00 SG D:CYS81 2.4 74.2 1.0 SG D:CYS84 2.4 68.3 1.0 SG D:CYS104 2.5 48.4 1.0 SG D:CYS107 2.5 72.0 1.0 CB D:CYS81 3.1 78.6 1.0 CB D:CYS107 3.3 65.2 1.0 N D:CYS84 3.4 80.0 1.0 CB D:CYS104 3.6 48.9 1.0 CB D:CYS84 3.7 77.4 1.0 N D:CYS104 3.8 53.2 1.0 CB D:GLU83 3.9 85.7 1.0 CA D:CYS84 4.1 73.5 1.0 CA D:CYS104 4.3 49.9 1.0 C D:GLU83 4.5 82.5 1.0 CA D:CYS81 4.5 75.8 1.0 CA D:GLU83 4.5 82.1 1.0 CA D:CYS107 4.6 69.6 1.0 CG D:GLU83 4.6 98.4 1.0 N D:GLU83 4.6 79.0 1.0 N D:SER85 4.6 73.2 1.0 N D:CYS107 4.6 64.5 1.0 NH1 D:ARG50 4.7 67.9 1.0 O D:CYS81 4.7 83.2 1.0 C D:CYS81 4.7 81.0 1.0 O D:CYS104 4.8 57.2 1.0 C D:CYS84 4.8 72.2 1.0 C D:LEU103 4.9 62.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:56.1 occ:1.00 SG D:CYS92 2.4 74.3 1.0 SG D:CYS64 2.4 59.0 1.0 SG D:CYS89 2.5 66.0 1.0 SG D:CYS67 2.5 62.2 1.0 CB D:CYS64 3.1 62.1 1.0 CB D:CYS67 3.2 53.2 1.0 CB D:CYS92 3.4 82.7 1.0 CB D:CYS89 3.5 63.0 1.0 N D:CYS67 3.5 59.1 1.0 N D:CYS89 3.8 63.0 1.0 CA D:CYS67 3.9 57.3 1.0 CA D:CYS89 4.2 62.5 1.0 CA D:CYS64 4.6 61.5 1.0 N D:CYS92 4.6 78.1 1.0 CA D:CYS92 4.6 83.1 1.0 O D:CYS89 4.6 60.3 1.0 C D:ARG66 4.6 65.3 1.0 CB D:ARG66 4.7 73.5 1.0 N D:LEU68 4.7 57.4 1.0 C D:CYS67 4.7 59.2 1.0 C D:CYS89 4.8 65.1 1.0 C D:VAL88 4.9 63.3 1.0 N D:ARG66 4.9 64.8 1.0 CB D:VAL88 5.0 62.6 1.0 CA D:ARG66 5.0 65.9 1.0

M.Kukimoto-Niino, A.Sakamoto, E.Kanno, K.Hanawa-Suetsugu, T.Terada, M.Shirouzu, M.Fukuda, S.Yokoyama. Structural Basis For the Exclusive Specificity of SLAC2-A/Melanophilin For the RAB27 Gtpases. Structure V. 16 1478 2008.
ISSN: ISSN 0969-2126
PubMed: 18940604
DOI: 10.1016/J.STR.2008.07.014