Zinc in PDB 3kdk: Structure of the C-Terminal Domain of Bacillus Subtilis Mutl Bound to ZN2+

The structure of Structure of the C-Terminal Domain of Bacillus Subtilis Mutl Bound to ZN2+, PDB code: 3kdk was solved by A.Guarne, M.C.Pillon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.75 / 2.26
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	33.231, 74.608, 182.244, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 26.9

The binding sites of Zinc atom in the Structure of the C-Terminal Domain of Bacillus Subtilis Mutl Bound to ZN2+ (pdb code 3kdk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the C-Terminal Domain of Bacillus Subtilis Mutl Bound to ZN2+, PDB code: 3kdk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of the C-Terminal Domain of Bacillus Subtilis Mutl Bound to ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the C-Terminal Domain of Bacillus Subtilis Mutl Bound to ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:64.0 occ:0.94 OE2 A:GLU468 2.2 45.9 1.0 O A:HOH628 2.4 50.9 1.0 ND1 A:HIS606 2.5 62.2 1.0 SG A:CYS604 2.5 44.6 1.0 CD A:GLU468 3.1 54.1 1.0 CG A:HIS606 3.1 59.5 1.0 CB A:HIS606 3.2 49.7 1.0 NH2 A:ARG608 3.3 91.5 1.0 OE1 A:GLU468 3.3 61.2 1.0 CE1 A:HIS606 3.5 61.4 1.0 CB A:CYS604 3.6 26.3 1.0 N A:HIS606 4.1 40.6 1.0 CA A:HIS606 4.3 42.4 1.0 CD2 A:HIS606 4.3 62.9 1.0 NE2 A:HIS606 4.4 66.2 1.0 CG A:GLU468 4.5 46.9 1.0 CZ A:ARG608 4.5 92.2 1.0 CB A:GLU468 4.8 35.2 1.0 CD A:PRO605 4.8 54.0 1.0 CD A:ARG608 4.9 72.5 1.0 CB A:ARG608 4.9 53.0 1.0 CA A:CYS604 4.9 42.8 1.0 N A:PRO605 4.9 52.2 1.0 C A:CYS604 4.9 42.5 1.0

Zinc binding site 2 out of 4 in the Structure of the C-Terminal Domain of Bacillus Subtilis Mutl Bound to ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the C-Terminal Domain of Bacillus Subtilis Mutl Bound to ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:78.7 occ:0.79 OE1 A:GLU468 2.2 61.2 1.0 NE2 A:HIS464 2.3 52.4 1.0 SG A:CYS573 2.9 0.7 1.0 CD A:GLU468 3.2 54.1 1.0 CE1 A:HIS464 3.3 54.4 1.0 CD2 A:HIS464 3.4 44.3 1.0 CG A:GLU468 3.6 46.9 1.0 CB A:CYS573 3.7 96.4 1.0 OE2 A:GLU468 4.4 45.9 1.0 ND1 A:HIS464 4.4 56.4 1.0 CA A:CYS573 4.4 94.6 1.0 CG A:HIS464 4.5 44.4 1.0 O A:HOH628 4.5 50.9 1.0

Zinc binding site 3 out of 4 in the Structure of the C-Terminal Domain of Bacillus Subtilis Mutl Bound to ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the C-Terminal Domain of Bacillus Subtilis Mutl Bound to ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3 b:52.4 occ:0.89 OE1 B:GLU468 2.0 54.7 1.0 ND1 B:HIS606 2.3 47.4 1.0 O B:HOH53 2.4 29.9 1.0 SG B:CYS604 2.4 36.3 1.0 CD B:GLU468 2.9 56.0 1.0 OE2 B:GLU468 3.1 50.6 1.0 CE1 B:HIS606 3.2 43.8 1.0 CG B:HIS606 3.2 44.3 1.0 CB B:CYS604 3.4 25.6 1.0 CB B:HIS606 3.5 35.5 1.0 N B:HIS606 4.1 42.9 1.0 CG B:GLU468 4.3 48.1 1.0 NE2 B:HIS606 4.3 46.1 1.0 CD2 B:HIS606 4.4 47.3 1.0 NH1 B:ARG608 4.4 80.6 1.0 CA B:HIS606 4.4 37.1 1.0 CD B:PRO605 4.5 36.9 1.0 CB B:GLU468 4.6 33.8 1.0 CA B:CYS604 4.7 34.2 1.0 N B:PRO605 4.7 42.9 1.0 C B:CYS604 4.9 44.3 1.0

Zinc binding site 4 out of 4 in the Structure of the C-Terminal Domain of Bacillus Subtilis Mutl Bound to ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the C-Terminal Domain of Bacillus Subtilis Mutl Bound to ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4 b:76.5 occ:0.83 OE2 B:GLU468 2.2 50.6 1.0 NE2 B:HIS464 2.2 63.2 1.0 SG B:CYS573 2.7 68.3 0.3 O B:HOH2 2.8 46.5 1.0 CE1 B:HIS464 3.0 61.3 1.0 CD B:GLU468 3.1 56.0 1.0 CD2 B:HIS464 3.3 54.9 1.0 CG B:GLU468 3.5 48.1 1.0 CB B:CYS573 3.6 64.2 0.7 CB B:CYS573 4.0 60.7 0.3 CA B:CYS573 4.2 62.7 0.7 ND1 B:HIS464 4.2 49.9 1.0 CA B:CYS573 4.2 62.1 0.3 OE1 B:GLU468 4.3 54.7 1.0 CG B:HIS464 4.3 48.8 1.0 O B:CYS573 4.6 69.3 0.3 O B:CYS573 4.8 69.2 0.7 C B:CYS573 4.8 67.2 0.3 CE1 B:HIS606 4.9 43.8 1.0 C B:CYS573 4.9 67.2 0.7 CB B:GLU468 4.9 33.8 1.0

M.C.Pillon, J.J.Lorenowicz, M.Uckelmann, A.D.Klocko, R.R.Mitchell, Y.S.Chung, P.Modrich, G.C.Walker, L.A.Simmons, P.Friedhoff, A.Guarne. Structure of the Endonuclease Domain of Mutl: Unlicensed to Cut. Mol.Cell V. 39 145 2010.
ISSN: ISSN 1097-2765
PubMed: 20603082
DOI: 10.1016/J.MOLCEL.2010.06.027