Zinc in PDB 4b6d: Structure of the Atypical C1 Domain of Mgcracgap

The structure of Structure of the Atypical C1 Domain of Mgcracgap, PDB code: 4b6d was solved by V.E.Pye, S.Lekomtsev, M.Petronczki, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.925 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.850, 133.850, 56.682, 90.00, 109.03, 90.00
R / Rfree (%)	21.03 / 23.55

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Structure of the Atypical C1 Domain of Mgcracgap (pdb code 4b6d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Structure of the Atypical C1 Domain of Mgcracgap, PDB code: 4b6d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Structure of the Atypical C1 Domain of Mgcracgap


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 Atypical C1 Domain of Mgcracgap within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1340 b:43.5 occ:1.00 ND1 A:HIS324 2.1 37.1 1.0 SG A:CYS303 2.3 47.1 1.0 SG A:CYS327 2.3 42.5 1.0 SG A:CYS300 2.3 33.3 1.0 CE1 A:HIS324 3.0 36.0 1.0 CG A:HIS324 3.1 34.0 1.0 CB A:CYS300 3.2 34.0 1.0 CB A:CYS303 3.2 45.3 1.0 CB A:CYS327 3.3 37.9 1.0 O A:HOH2018 3.4 63.4 1.0 CB A:HIS324 3.5 36.2 1.0 N A:CYS303 4.0 41.8 1.0 N A:HIS324 4.1 33.5 1.0 NE2 A:HIS324 4.1 35.3 1.0 CA A:CYS303 4.2 44.0 1.0 CD2 A:HIS324 4.2 35.6 1.0 CA A:HIS324 4.4 33.7 1.0 OG A:SER323 4.5 59.8 1.0 CA A:CYS300 4.6 34.3 1.0 CA A:CYS327 4.7 41.2 1.0 CG A:PRO302 4.9 35.6 1.0 C A:CYS303 5.0 45.7 1.0

Zinc binding site 2 out of 12 in the Structure of the Atypical C1 Domain of Mgcracgap


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 Atypical C1 Domain of Mgcracgap within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1341 b:39.3 occ:1.00 ND1 A:HIS287 2.0 37.8 1.0 SG A:CYS319 2.2 45.2 1.0 SG A:CYS316 2.3 53.8 1.0 SG A:CYS335 2.3 68.4 1.0 CE1 A:HIS287 2.8 41.5 1.0 CG A:HIS287 3.2 36.7 1.0 CB A:CYS316 3.3 41.4 1.0 CB A:CYS335 3.4 42.3 1.0 CB A:CYS319 3.4 36.4 1.0 CB A:HIS287 3.7 38.6 1.0 N A:CYS319 3.8 45.9 1.0 CA A:HIS287 3.8 30.8 1.0 NE2 A:HIS287 4.0 30.2 1.0 O2 A:GOL1339 4.1 34.4 1.0 CA A:CYS319 4.2 43.8 1.0 CA A:CYS335 4.2 40.9 1.0 CD2 A:HIS287 4.2 34.3 1.0 CB A:ASP318 4.6 55.6 1.0 C1 A:GOL1339 4.6 29.4 1.0 N A:ASP288 4.7 40.4 1.0 C A:ASP318 4.7 48.5 1.0 CA A:CYS316 4.7 42.6 1.0 CB A:VAL321 4.7 34.0 1.0 N A:HIS287 4.8 33.2 1.0 C A:HIS287 4.8 39.9 1.0 C A:CYS319 4.9 43.7 1.0 C A:CYS335 4.9 41.5 1.0 CG2 A:VAL321 4.9 33.8 1.0

Zinc binding site 3 out of 12 in the Structure of the Atypical C1 Domain of Mgcracgap


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 Atypical C1 Domain of Mgcracgap within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1339 b:59.3 occ:1.00 ND1 B:HIS324 2.1 53.2 1.0 SG B:CYS303 2.3 45.8 1.0 SG B:CYS300 2.3 47.8 1.0 SG B:CYS327 2.4 42.6 1.0 CE1 B:HIS324 3.0 53.0 1.0 CG B:HIS324 3.1 51.3 1.0 CB B:CYS303 3.1 64.8 1.0 CB B:CYS300 3.2 56.1 1.0 CB B:HIS324 3.4 47.3 1.0 CB B:CYS327 3.4 50.0 1.0 N B:CYS303 4.0 66.1 1.0 N B:HIS324 4.0 48.4 1.0 CA B:CYS303 4.1 66.3 1.0 NE2 B:HIS324 4.1 53.9 1.0 O B:HOH2017 4.1 33.3 1.0 CD2 B:HIS324 4.2 53.3 1.0 CA B:HIS324 4.4 47.4 1.0 NH2 B:ARG330 4.5 53.9 1.0 CA B:CYS300 4.7 57.5 1.0 OG B:SER323 4.7 50.0 1.0 CA B:CYS327 4.8 49.7 1.0 C B:CYS303 4.9 68.6 1.0 CG B:PRO302 4.9 57.1 1.0

Zinc binding site 4 out of 12 in the Structure of the Atypical C1 Domain of Mgcracgap


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 Atypical C1 Domain of Mgcracgap within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1340 b:50.8 occ:1.00 ND1 B:HIS287 2.0 55.8 1.0 SG B:CYS335 2.3 50.4 1.0 SG B:CYS316 2.3 44.4 1.0 SG B:CYS319 2.4 49.1 1.0 CE1 B:HIS287 2.9 54.1 1.0 CG B:HIS287 3.1 53.6 1.0 CB B:CYS316 3.2 41.7 1.0 CB B:CYS335 3.2 37.6 1.0 CB B:HIS287 3.6 53.6 1.0 CB B:CYS319 3.6 54.7 1.0 CA B:HIS287 3.8 52.7 1.0 N B:CYS319 3.9 55.5 1.0 CA B:CYS335 4.0 37.0 1.0 NE2 B:HIS287 4.0 52.2 1.0 CD2 B:HIS287 4.2 51.7 1.0 CA B:CYS319 4.3 57.7 1.0 CB B:ASP318 4.6 62.5 1.0 N B:ASP288 4.6 52.1 1.0 CA B:CYS316 4.7 58.2 1.0 C B:CYS335 4.7 42.4 1.0 CB B:VAL321 4.7 60.1 1.0 N B:ILE336 4.7 43.4 1.0 N B:HIS287 4.7 52.4 1.0 C B:ASP318 4.8 57.6 1.0 C B:HIS287 4.8 52.6 1.0 O B:HOH2020 4.8 44.0 1.0 C B:CYS319 4.9 63.7 1.0 N B:ASP318 4.9 66.9 1.0 CG2 B:VAL321 5.0 61.0 1.0 O B:LEU286 5.0 51.3 1.0 O B:CYS319 5.0 63.9 1.0

Zinc binding site 5 out of 12 in the Structure of the Atypical C1 Domain of Mgcracgap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Atypical C1 Domain of Mgcracgap within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1339 b:43.0 occ:1.00 ND1 C:HIS324 2.1 43.8 1.0 SG C:CYS303 2.3 56.7 1.0 SG C:CYS327 2.3 43.9 1.0 SG C:CYS300 2.3 37.0 1.0 CE1 C:HIS324 3.0 45.2 1.0 CG C:HIS324 3.1 39.3 1.0 CB C:CYS300 3.1 45.3 1.0 CB C:CYS303 3.3 51.1 1.0 CB C:CYS327 3.3 48.9 1.0 O C:HOH2014 3.4 36.6 1.0 CB C:HIS324 3.4 37.4 1.0 N C:HIS324 3.9 37.5 1.0 N C:CYS303 4.1 46.4 1.0 NE2 C:HIS324 4.1 44.1 1.0 CD2 C:HIS324 4.2 42.3 1.0 CA C:CYS303 4.2 50.8 1.0 CA C:HIS324 4.3 36.7 1.0 CA C:CYS300 4.6 45.3 1.0 CA C:CYS327 4.7 51.2 1.0 CG C:PRO302 4.9 40.7 1.0

Zinc binding site 6 out of 12 in the Structure of the Atypical C1 Domain of Mgcracgap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Atypical C1 Domain of Mgcracgap within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1340 b:39.7 occ:1.00 ND1 C:HIS287 2.0 35.8 1.0 SG C:CYS319 2.2 45.4 1.0 SG C:CYS335 2.2 43.4 1.0 SG C:CYS316 2.4 46.6 1.0 CE1 C:HIS287 2.8 35.5 1.0 CG C:HIS287 3.2 36.3 1.0 CB C:CYS335 3.2 39.9 1.0 CB C:CYS316 3.4 43.0 1.0 CB C:CYS319 3.4 39.5 1.0 N C:CYS319 3.7 41.3 1.0 CB C:HIS287 3.7 36.0 1.0 CA C:HIS287 3.9 36.8 1.0 NE2 C:HIS287 4.0 33.0 1.0 CA C:CYS335 4.0 39.6 1.0 CA C:CYS319 4.1 41.2 1.0 CD2 C:HIS287 4.2 34.3 1.0 CB C:ASP318 4.6 47.6 1.0 CB C:VAL321 4.6 37.4 1.0 C C:ASP318 4.6 42.0 1.0 C C:CYS335 4.7 41.3 1.0 C C:CYS319 4.7 42.6 1.0 N C:ILE336 4.7 42.6 1.0 N C:ASP288 4.7 43.9 1.0 CA C:CYS316 4.8 43.3 1.0 N C:HIS287 4.8 37.8 1.0 CG2 C:VAL321 4.8 36.1 1.0 C C:HIS287 4.9 41.7 1.0 O C:HOH2029 5.0 27.4 1.0 CA C:ASP318 5.0 44.2 1.0 N C:ASP318 5.0 44.6 1.0 O C:CYS319 5.0 44.2 1.0

Zinc binding site 7 out of 12 in the Structure of the Atypical C1 Domain of Mgcracgap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the Atypical C1 Domain of Mgcracgap within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1339 b:46.3 occ:1.00 ND1 D:HIS324 2.1 58.7 1.0 SG D:CYS300 2.2 47.1 1.0 SG D:CYS303 2.3 65.0 1.0 SG D:CYS327 2.4 55.8 1.0 CB D:CYS300 2.9 47.7 1.0 CE1 D:HIS324 3.0 57.0 1.0 CG D:HIS324 3.1 55.3 1.0 CB D:CYS303 3.3 50.6 1.0 CB D:CYS327 3.3 53.8 1.0 CB D:HIS324 3.5 49.4 1.0 N D:HIS324 4.0 54.1 1.0 N D:CYS303 4.1 50.1 1.0 NE2 D:HIS324 4.1 55.6 1.0 CD2 D:HIS324 4.2 55.0 1.0 CA D:CYS303 4.2 51.0 1.0 CA D:CYS300 4.4 47.9 1.0 CA D:HIS324 4.4 54.3 1.0 CA D:CYS327 4.7 56.0 1.0 C D:CYS300 4.9 49.2 1.0 CG D:PRO302 4.9 45.8 1.0 C D:CYS303 5.0 53.9 1.0 O D:HOH2021 5.0 57.0 1.0

Zinc binding site 8 out of 12 in the Structure of the Atypical C1 Domain of Mgcracgap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of the Atypical C1 Domain of Mgcracgap within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1340 b:53.2 occ:1.00 ND1 D:HIS287 2.0 51.7 1.0 SG D:CYS319 2.2 52.7 1.0 SG D:CYS335 2.3 54.9 1.0 SG D:CYS316 2.3 49.1 1.0 CE1 D:HIS287 2.9 53.7 1.0 CG D:HIS287 3.1 51.5 1.0 CB D:CYS316 3.2 47.8 1.0 CB D:CYS335 3.2 59.5 1.0 CB D:CYS319 3.4 58.2 1.0 CB D:HIS287 3.6 53.9 1.0 CA D:HIS287 3.8 56.6 1.0 N D:CYS319 3.8 64.8 1.0 CA D:CYS335 4.0 57.5 1.0 NE2 D:HIS287 4.0 51.7 1.0 CA D:CYS319 4.1 61.6 1.0 CD2 D:HIS287 4.2 49.9 1.0 N D:ASP288 4.6 60.3 1.0 CB D:ASP318 4.6 65.3 1.0 CA D:CYS316 4.7 53.0 1.0 C D:ASP318 4.7 66.9 1.0 N D:HIS287 4.7 53.4 1.0 C D:CYS335 4.7 59.5 1.0 C D:HIS287 4.8 61.9 1.0 CB D:VAL321 4.8 55.7 1.0 C D:CYS319 4.8 60.7 1.0 N D:ILE336 4.8 62.2 1.0 CG2 D:VAL321 4.9 57.1 1.0

Zinc binding site 9 out of 12 in the Structure of the Atypical C1 Domain of Mgcracgap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of the Atypical C1 Domain of Mgcracgap within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1339 b:50.6 occ:1.00 ND1 E:HIS324 2.1 64.5 1.0 SG E:CYS303 2.3 49.3 1.0 SG E:CYS300 2.3 45.5 1.0 SG E:CYS327 2.3 52.0 1.0 CB E:CYS300 3.0 47.3 1.0 CE1 E:HIS324 3.0 65.6 1.0 CG E:HIS324 3.1 62.3 1.0 CB E:CYS303 3.1 47.3 1.0 CB E:CYS327 3.2 47.6 1.0 CB E:HIS324 3.4 56.5 1.0 N E:CYS303 4.0 51.0 1.0 N E:HIS324 4.1 53.0 1.0 NE2 E:HIS324 4.1 66.5 1.0 CA E:CYS303 4.1 49.1 1.0 CD2 E:HIS324 4.2 64.9 1.0 OG E:SER323 4.2 53.7 1.0 CA E:HIS324 4.4 53.1 1.0 NH2 E:ARG330 4.4 73.6 1.0 CA E:CYS300 4.5 48.6 1.0 NZ E:LYS305 4.6 45.1 1.0 CA E:CYS327 4.7 48.4 1.0 C E:CYS303 4.9 51.6 1.0 CG E:PRO302 4.9 48.2 1.0 C E:CYS300 4.9 51.6 1.0

Zinc binding site 10 out of 12 in the Structure of the Atypical C1 Domain of Mgcracgap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of the Atypical C1 Domain of Mgcracgap within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1340 b:56.8 occ:1.00 ND1 E:HIS287 2.0 38.7 1.0 SG E:CYS335 2.3 43.9 1.0 SG E:CYS316 2.3 84.6 1.0 SG E:CYS319 2.3 47.2 1.0 CE1 E:HIS287 2.9 36.9 1.0 CB E:CYS316 3.1 57.2 1.0 CG E:HIS287 3.1 36.4 1.0 CB E:CYS335 3.1 47.0 1.0 CB E:CYS319 3.6 54.5 1.0 CB E:HIS287 3.6 37.1 1.0 CA E:HIS287 3.8 40.4 1.0 CA E:CYS335 3.8 44.6 1.0 N E:CYS319 3.9 62.5 1.0 NE2 E:HIS287 4.0 33.3 1.0 O E:HOH2018 4.1 32.7 1.0 CD2 E:HIS287 4.2 33.4 1.0 CA E:CYS319 4.3 59.9 1.0 CB E:ASP318 4.5 79.3 1.0 CA E:CYS316 4.6 60.7 1.0 C E:CYS335 4.6 43.5 1.0 N E:ILE336 4.7 43.9 1.0 N E:HIS287 4.7 41.1 1.0 N E:ASP288 4.7 42.7 1.0 CB E:VAL321 4.7 55.2 1.0 C E:ASP318 4.8 67.4 1.0 C E:HIS287 4.8 41.0 1.0 N E:ASP318 4.9 84.7 1.0 CG2 E:VAL321 4.9 57.6 1.0 CA E:ASP318 5.0 77.7 1.0 C E:CYS319 5.0 62.0 1.0

S.Lekomtsev, K.Su, V.E.Pye, K.Blight, S.Sundaramoorthy, T.Takaki, L.M.Collinson, P.Cherepanov, N.Divecha, M.Petronczki. Centralspindlin Links the Mitotic Spindle to the Plasma Membrane During Cytokinesis. Nature V. 492 276 2012.
ISSN: ISSN 0028-0836
PubMed: 23235882
DOI: 10.1038/NATURE11773