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Zinc in PDB 7sfz: Crystal Structure of MIS18A-Yippee Domain

Protein crystallography data

The structure of Crystal Structure of MIS18A-Yippee Domain, PDB code: 7sfz was solved by S.H.Park, U.Cho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.99 / 3.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.725, 114.864, 116.27, 90, 90, 90
R / Rfree (%) 20.3 / 25

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of MIS18A-Yippee Domain (pdb code 7sfz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of MIS18A-Yippee Domain, PDB code: 7sfz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7sfz

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Zinc binding site 1 out of 8 in the Crystal Structure of MIS18A-Yippee Domain


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 MIS18A-Yippee Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:95.1
occ:1.00
 SG B:CYS88 2.2 60.6 1.0
SG B:CYS85 2.3 57.3 1.0
SG B:CYS144 2.4 55.6 1.0
SG B:CYS141 2.4 50.8 1.0
CB B:CYS85 3.2 50.8 1.0
CB B:CYS144 3.3 61.5 1.0
CB B:CYS141 3.3 59.8 1.0
CB B:CYS88 3.4 56.7 1.0
N B:CYS88 3.5 52.6 1.0
N B:CYS144 3.9 51.6 1.0
CA B:CYS88 4.0 52.2 1.0
CA B:CYS144 4.2 61.9 1.0
C B:GLY87 4.3 63.1 1.0
CA B:GLY87 4.5 61.0 1.0
N B:GLY87 4.6 58.8 1.0
CA B:CYS85 4.7 47.8 1.0
C B:CYS88 4.7 51.4 1.0
CA B:CYS141 4.8 60.0 1.0
C B:GLY143 4.8 52.9 1.0
C B:CYS144 4.8 68.0 1.0
CB B:LEU146 4.9 56.7 1.0
NH1 B:ARG90 5.0 51.6 1.0
CB B:ARG90 5.0 45.4 1.0

Zinc binding site 2 out of 8 in 7sfz

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Zinc binding site 2 out of 8 in the Crystal Structure of MIS18A-Yippee Domain


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 MIS18A-Yippee Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:60.9
occ:1.00
 SG A:CYS85 2.1 59.9 1.0
SG A:CYS88 2.1 83.0 1.0
SG A:CYS144 2.2 87.1 1.0
SG A:CYS141 2.3 54.3 1.0
CB A:CYS141 3.2 54.5 1.0
CB A:CYS85 3.2 51.9 1.0
CB A:CYS144 3.5 82.1 1.0
CB A:CYS88 3.5 74.9 1.0
N A:CYS144 3.6 57.7 1.0
N A:CYS88 3.8 51.7 1.0
CA A:CYS144 4.1 69.1 1.0
CA A:CYS88 4.2 58.2 1.0
C A:GLY87 4.4 72.5 1.0
C A:GLY143 4.5 59.0 1.0
CA A:CYS141 4.6 57.0 1.0
N A:GLY87 4.6 56.5 1.0
CA A:CYS85 4.7 51.7 1.0
CA A:GLY143 4.7 57.5 1.0
CA A:GLY87 4.7 63.5 1.0
CB A:LEU146 4.8 56.8 1.0
N A:GLY143 4.8 59.4 1.0
C A:CYS144 4.9 68.2 1.0
O A:CYS141 4.9 58.1 1.0
N A:SER145 4.9 64.6 1.0
C A:CYS88 4.9 59.0 1.0
NE A:ARG90 4.9 62.9 1.0
C A:CYS141 5.0 55.8 1.0

Zinc binding site 3 out of 8 in 7sfz

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Zinc binding site 3 out of 8 in the Crystal Structure of MIS18A-Yippee Domain


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 MIS18A-Yippee Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:65.5
occ:1.00
 SG C:CYS88 2.2 86.8 1.0
SG C:CYS144 2.2 89.4 1.0
SG C:CYS141 2.3 60.1 1.0
SG C:CYS85 2.4 68.2 1.0
CB C:CYS141 3.1 62.8 1.0
CB C:CYS144 3.3 78.8 1.0
CB C:CYS85 3.4 63.4 1.0
CB C:CYS88 3.5 77.6 1.0
N C:CYS88 3.5 74.4 1.0
N C:CYS144 3.7 66.9 1.0
CA C:CYS144 4.1 71.8 1.0
CA C:CYS88 4.1 70.7 1.0
C C:GLY87 4.3 75.8 1.0
CA C:GLY87 4.3 72.1 1.0
N C:GLY87 4.5 73.7 1.0
CA C:CYS141 4.6 64.8 1.0
C C:GLY143 4.7 73.2 1.0
CB C:LEU146 4.7 65.3 1.0
C C:CYS144 4.8 78.2 1.0
CA C:CYS85 4.8 64.8 1.0
C C:CYS88 4.9 67.5 1.0
N C:ARG89 4.9 65.6 1.0
CA C:GLY143 4.9 67.8 1.0

Zinc binding site 4 out of 8 in 7sfz

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Zinc binding site 4 out of 8 in the Crystal Structure of MIS18A-Yippee Domain


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 MIS18A-Yippee Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:65.4
occ:1.00
 SG D:CYS144 2.2 71.8 1.0
SG D:CYS88 2.3 78.3 1.0
SG D:CYS85 2.3 63.6 1.0
SG D:CYS141 2.4 75.5 1.0
CB D:CYS144 3.0 77.1 1.0
CB D:CYS141 3.1 76.4 1.0
CB D:CYS85 3.3 60.6 1.0
CB D:CYS88 3.7 73.9 1.0
N D:CYS144 3.8 82.4 1.0
N D:CYS88 3.8 62.7 1.0
CA D:CYS144 3.9 81.0 1.0
CA D:CYS88 4.3 65.7 1.0
C D:CYS144 4.5 82.9 1.0
CA D:CYS141 4.6 78.8 1.0
C D:GLY87 4.6 64.4 1.0
CA D:GLY87 4.6 59.2 1.0
CA D:CYS85 4.7 56.6 1.0
N D:SER145 4.8 82.6 1.0
N D:GLY87 4.8 55.5 1.0
CB D:LEU146 4.8 65.4 1.0
C D:GLY143 4.8 87.5 1.0
C D:CYS88 4.9 63.5 1.0
N D:ARG89 4.9 58.5 1.0
CB D:ARG90 5.0 71.7 1.0
N D:LEU146 5.0 74.4 1.0

Zinc binding site 5 out of 8 in 7sfz

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Zinc binding site 5 out of 8 in the Crystal Structure of MIS18A-Yippee Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of MIS18A-Yippee Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:85.3
occ:1.00
 SG E:CYS144 2.3 81.8 1.0
SG E:CYS88 2.3 115.3 1.0
SG E:CYS141 2.4 69.5 1.0
SG E:CYS85 2.5 75.6 1.0
CB E:CYS144 3.1 80.8 1.0
CB E:CYS141 3.2 74.7 1.0
N E:CYS88 3.2 85.3 1.0
CB E:CYS88 3.4 107.7 1.0
CB E:CYS85 3.5 72.4 1.0
N E:CYS144 3.6 79.8 1.0
CA E:CYS88 3.7 82.2 1.0
CA E:CYS144 3.9 82.7 1.0
C E:GLY87 4.0 98.7 1.0
CA E:GLY87 4.2 94.5 1.0
N E:GLY87 4.4 90.4 1.0
C E:CYS88 4.5 80.9 1.0
N E:ARG89 4.6 78.5 1.0
CA E:CYS141 4.6 75.7 1.0
C E:CYS144 4.7 81.2 1.0
C E:GLY143 4.7 81.1 1.0
NH1 E:ARG90 4.9 77.6 1.0
N E:SER145 4.9 83.1 1.0
CA E:CYS85 5.0 74.0 1.0
O E:GLY87 5.0 108.6 1.0
CA E:GLY143 5.0 75.7 1.0
N E:GLY143 5.0 75.8 1.0

Zinc binding site 6 out of 8 in 7sfz

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Zinc binding site 6 out of 8 in the Crystal Structure of MIS18A-Yippee Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of MIS18A-Yippee Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:98.4
occ:1.00
 SG F:CYS144 2.2 75.1 1.0
SG F:CYS85 2.2 58.7 1.0
SG F:CYS88 2.4 110.7 1.0
SG F:CYS141 2.4 91.3 1.0
CB F:CYS141 3.2 81.5 1.0
CB F:CYS144 3.3 75.6 1.0
CB F:CYS85 3.4 65.7 1.0
CB F:CYS88 3.5 82.9 1.0
N F:CYS144 3.6 76.0 1.0
N F:CYS88 3.6 56.7 1.0
CA F:CYS144 4.0 76.7 1.0
CA F:CYS88 4.2 57.5 1.0
C F:GLY87 4.4 60.4 1.0
CA F:GLY87 4.5 58.6 1.0
N F:GLY87 4.7 56.8 1.0
CA F:CYS141 4.7 79.1 1.0
CB F:LEU146 4.7 60.8 1.0
C F:CYS144 4.7 80.8 1.0
CA F:CYS85 4.7 65.0 1.0
C F:GLY143 4.7 82.2 1.0
C F:CYS88 4.8 62.5 1.0
CD F:ARG90 4.9 67.8 1.0
O F:CYS85 4.9 66.1 1.0
N F:SER145 4.9 82.8 1.0
N F:ARG89 4.9 55.8 1.0
CB F:ARG90 5.0 54.8 1.0
C F:CYS85 5.0 68.0 1.0
CA F:GLY143 5.0 81.2 1.0

Zinc binding site 7 out of 8 in 7sfz

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Zinc binding site 7 out of 8 in the Crystal Structure of MIS18A-Yippee Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of MIS18A-Yippee Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn201

b:82.1
occ:1.00
 SG G:CYS144 2.2 110.0 1.0
SG G:CYS88 2.4 125.0 1.0
SG G:CYS85 2.4 69.1 1.0
SG G:CYS141 2.6 87.7 1.0
CB G:CYS144 3.0 99.9 1.0
CB G:CYS141 3.2 76.9 1.0
N G:CYS88 3.3 69.5 1.0
CB G:CYS85 3.4 62.2 1.0
CB G:CYS88 3.6 111.7 1.0
N G:CYS144 3.7 73.7 1.0
CA G:CYS144 3.8 79.0 1.0
CA G:CYS88 4.0 82.8 1.0
C G:GLY87 4.3 72.2 1.0
CA G:GLY87 4.4 69.5 1.0
C G:CYS144 4.5 78.6 1.0
N G:GLY87 4.6 68.3 1.0
C G:CYS88 4.7 69.4 1.0
N G:SER145 4.7 79.9 1.0
CA G:CYS141 4.7 74.8 1.0
NH1 G:ARG90 4.8 70.3 1.0
C G:GLY143 4.8 77.2 1.0
N G:ARG89 4.8 60.7 1.0
CA G:CYS85 4.9 55.1 1.0
CB G:LEU146 4.9 74.3 1.0

Zinc binding site 8 out of 8 in 7sfz

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Zinc binding site 8 out of 8 in the Crystal Structure of MIS18A-Yippee Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of MIS18A-Yippee Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn201

b:88.8
occ:1.00
 SG H:CYS85 2.3 63.4 1.0
SG H:CYS88 2.5 79.6 1.0
SG H:CYS141 2.5 79.0 1.0
CB H:CYS144 2.5 75.2 1.0
SG H:CYS144 2.6 75.7 1.0
CB H:CYS141 3.1 82.6 1.0
CB H:CYS85 3.3 59.8 1.0
N H:CYS88 3.5 64.4 1.0
CB H:CYS88 3.6 81.3 1.0
CA H:CYS144 3.9 83.1 1.0
CA H:CYS88 4.1 71.1 1.0
C H:GLY87 4.3 76.5 1.0
N H:CYS144 4.3 86.8 1.0
CA H:GLY87 4.4 75.0 1.0
N H:GLY87 4.5 68.0 1.0
C H:CYS144 4.6 90.8 1.0
CA H:CYS141 4.6 74.2 1.0
CA H:CYS85 4.6 60.9 1.0
CB H:LEU146 4.7 74.6 1.0
C H:CYS88 4.7 69.4 1.0
N H:ARG89 4.9 60.0 1.0
NE H:ARG90 4.9 82.5 1.0
N H:SER145 4.9 89.8 1.0
C H:CYS85 5.0 62.4 1.0

Reference:

S.H.Park, K.Shimanaka, U.Cho. Structural Basis For MIS18 Complex Assembly: Implications For Centromere Maintenance To Be Published.
Page generated: Wed Oct 30 11:11:42 2024

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