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Zinc in PDB 9iic: Crystal Structure of Hoip RING2-Ldd in Complex with STK4 Kd Domain

Enzymatic activity of Crystal Structure of Hoip RING2-Ldd in Complex with STK4 Kd Domain

All present enzymatic activity of Crystal Structure of Hoip RING2-Ldd in Complex with STK4 Kd Domain:
2.3.2.31;

Protein crystallography data

The structure of Crystal Structure of Hoip RING2-Ldd in Complex with STK4 Kd Domain, PDB code: 9iic was solved by Y.R.Wang, X.D.Zhou, L.F.Pan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.87 / 2.78
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 138.989, 96.363, 115.773, 90, 118.82, 90
R / Rfree (%) 23.7 / 28

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Hoip RING2-Ldd in Complex with STK4 Kd Domain (pdb code 9iic). 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 Hoip RING2-Ldd in Complex with STK4 Kd Domain, PDB code: 9iic:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 9iic

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Zinc binding site 1 out of 8 in the Crystal Structure of Hoip RING2-Ldd in Complex with STK4 Kd 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 Hoip RING2-Ldd in Complex with STK4 Kd Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1101

b:118.8
occ:1.00
 SG C:CYS890 2.3 114.3 1.0
SG C:CYS893 2.3 148.9 1.0
SG C:CYS871 2.3 119.5 1.0
SG C:CYS874 2.3 122.0 1.0
CB C:CYS890 3.2 114.6 1.0
CB C:CYS871 3.2 110.7 1.0
CB C:CYS874 3.4 128.9 1.0
N C:CYS874 3.5 129.4 1.0
CB C:CYS893 3.6 153.0 1.0
O C:CYS874 3.8 126.9 1.0
N C:CYS893 3.9 148.4 1.0
CA C:CYS874 3.9 130.7 1.0
CA C:CYS893 4.3 152.5 1.0
C C:CYS874 4.3 130.2 1.0
CB C:GLN892 4.4 121.5 1.0
CB C:LYS873 4.5 131.7 1.0
C C:LYS873 4.6 133.9 1.0
CA C:CYS890 4.6 114.4 1.0
CA C:CYS871 4.7 111.5 1.0
CB C:HIS895 4.7 127.2 1.0
C C:GLN892 4.7 129.8 1.0
N C:LYS873 4.9 127.3 1.0
C C:CYS893 4.9 153.7 1.0
CA C:LYS873 4.9 130.9 1.0
OH C:TYR878 5.0 110.1 1.0
CA C:GLN892 5.0 124.5 1.0
N C:GLN892 5.0 122.4 1.0

Zinc binding site 2 out of 8 in 9iic

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Zinc binding site 2 out of 8 in the Crystal Structure of Hoip RING2-Ldd in Complex with STK4 Kd 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 Hoip RING2-Ldd in Complex with STK4 Kd Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1102

b:85.9
occ:1.00
 ND1 C:HIS926 2.1 101.8 1.0
SG C:CYS901 2.3 117.0 1.0
SG C:CYS930 2.3 100.1 1.0
SG C:CYS898 2.3 132.6 1.0
CE1 C:HIS926 3.0 104.4 1.0
CB C:CYS901 3.2 112.3 1.0
CG C:HIS926 3.2 103.5 1.0
N C:CYS901 3.3 109.3 1.0
CB C:CYS898 3.4 133.6 1.0
CB C:CYS930 3.6 98.5 1.0
CB C:HIS926 3.6 102.3 1.0
CB C:PHE932 3.8 98.1 1.0
CA C:CYS901 3.8 109.1 1.0
NE2 C:HIS926 4.1 107.3 1.0
CD2 C:HIS926 4.3 107.2 1.0
C C:GLY900 4.3 106.5 1.0
CA C:HIS926 4.3 105.1 1.0
CA C:GLY900 4.5 107.4 1.0
CG C:PHE932 4.6 100.4 1.0
N C:GLY900 4.6 109.4 1.0
C C:CYS901 4.7 109.5 1.0
N C:PHE932 4.7 91.4 1.0
CA C:CYS898 4.8 133.4 1.0
CD C:PRO927 4.9 100.5 1.0
CA C:PHE932 4.9 97.1 1.0
N C:TYR902 4.9 114.1 1.0
ND2 C:ASN903 4.9 120.9 1.0
CA C:CYS930 4.9 94.3 1.0

Zinc binding site 3 out of 8 in 9iic

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Zinc binding site 3 out of 8 in the Crystal Structure of Hoip RING2-Ldd in Complex with STK4 Kd 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 Hoip RING2-Ldd in Complex with STK4 Kd Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1103

b:94.6
occ:1.00
 ND1 C:HIS1001 2.1 78.9 1.0
SG C:CYS998 2.3 99.1 1.0
SG C:CYS969 2.3 83.2 1.0
SG C:CYS986 2.3 104.1 1.0
CB C:CYS969 2.8 93.4 1.0
CE1 C:HIS1001 2.8 80.0 1.0
CB C:CYS986 3.2 99.3 1.0
CG C:HIS1001 3.2 75.5 1.0
CB C:CYS998 3.4 101.6 1.0
CB C:HIS1001 3.8 78.0 1.0
NE2 C:HIS1001 4.0 77.6 1.0
CD2 C:HIS1001 4.2 71.9 1.0
N C:CYS998 4.2 91.9 1.0
CA C:CYS969 4.2 106.0 1.0
CA C:CYS998 4.4 99.8 1.0
CB C:VAL971 4.6 77.1 1.0
CG2 C:VAL971 4.6 77.2 1.0
N C:HIS1001 4.6 80.0 1.0
CA C:CYS986 4.6 101.4 1.0
C C:CYS969 4.7 104.6 1.0
CB C:LYS988 4.8 118.9 1.0
CA C:HIS1001 4.9 77.8 1.0
OE2 C:GLU973 4.9 105.2 1.0
O C:CYS969 4.9 102.1 1.0
N C:LYS988 5.0 116.7 1.0
CE C:LYS988 5.0 116.8 1.0

Zinc binding site 4 out of 8 in 9iic

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Zinc binding site 4 out of 8 in the Crystal Structure of Hoip RING2-Ldd in Complex with STK4 Kd 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 Hoip RING2-Ldd in Complex with STK4 Kd Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1104

b:158.4
occ:1.00
 NE2 C:HIS923 2.1 147.2 1.0
NE2 C:HIS925 2.1 136.5 1.0
SG C:CYS916 2.3 187.7 1.0
SG C:CYS911 2.3 154.0 1.0
CE1 C:HIS925 3.0 136.6 1.0
CE1 C:HIS923 3.0 156.2 1.0
CD2 C:HIS923 3.0 142.2 1.0
CD2 C:HIS925 3.1 133.0 1.0
CB C:CYS911 3.2 158.4 1.0
CB C:CYS916 3.3 191.4 1.0
ND1 C:HIS923 4.1 156.9 1.0
ND1 C:HIS925 4.1 131.4 1.0
CA C:CYS916 4.1 190.8 1.0
CG C:HIS923 4.1 147.3 1.0
CG C:HIS925 4.2 128.8 1.0
CB C:GLU913 4.3 152.1 1.0
CA C:CYS911 4.7 159.9 1.0
O C:GLU913 4.8 163.2 1.0
CG2 C:VAL918 4.8 153.3 1.0

Zinc binding site 5 out of 8 in 9iic

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Zinc binding site 5 out of 8 in the Crystal Structure of Hoip RING2-Ldd in Complex with STK4 Kd 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 Hoip RING2-Ldd in Complex with STK4 Kd Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1101

b:130.6
occ:1.00
 SG D:CYS890 2.3 140.3 1.0
SG D:CYS874 2.3 142.0 1.0
SG D:CYS893 2.3 152.3 1.0
SG D:CYS871 2.3 146.6 1.0
CB D:CYS871 3.2 137.6 1.0
CB D:CYS890 3.4 141.8 1.0
CB D:CYS874 3.4 145.7 1.0
N D:CYS874 3.7 145.2 1.0
CB D:CYS893 3.7 156.6 1.0
N D:CYS893 4.0 152.3 1.0
CA D:CYS874 4.0 144.0 1.0
O D:CYS874 4.0 135.5 1.0
CA D:CYS893 4.3 157.0 1.0
C D:CYS874 4.5 138.6 1.0
CB D:GLN892 4.5 144.6 1.0
CA D:CYS871 4.6 134.9 1.0
CB D:LYS873 4.7 153.5 1.0
CB D:HIS895 4.7 154.2 1.0
C D:LYS873 4.7 150.0 1.0
CA D:CYS890 4.8 140.7 1.0
C D:GLN892 4.8 152.2 1.0
C D:CYS893 4.9 159.1 1.0
N D:GLN892 5.0 144.8 1.0

Zinc binding site 6 out of 8 in 9iic

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Zinc binding site 6 out of 8 in the Crystal Structure of Hoip RING2-Ldd in Complex with STK4 Kd 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 Hoip RING2-Ldd in Complex with STK4 Kd Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1102

b:131.2
occ:1.00
 ND1 D:HIS926 2.1 143.9 1.0
SG D:CYS901 2.3 140.4 1.0
SG D:CYS930 2.3 112.2 1.0
SG D:CYS898 2.3 144.6 1.0
CE1 D:HIS926 2.8 146.5 1.0
CB D:CYS901 3.1 134.4 1.0
CG D:HIS926 3.2 147.2 1.0
N D:CYS901 3.3 126.3 1.0
CB D:CYS898 3.4 145.3 1.0
CB D:CYS930 3.7 117.6 1.0
CB D:PHE932 3.7 125.0 1.0
CB D:HIS926 3.8 145.5 1.0
CA D:CYS901 3.8 129.4 1.0
NE2 D:HIS926 4.1 151.2 1.0
C D:GLY900 4.2 121.4 1.0
CD2 D:HIS926 4.3 151.2 1.0
CA D:GLY900 4.4 120.5 1.0
CA D:HIS926 4.5 148.1 1.0
CG D:PHE932 4.6 130.7 1.0
N D:PHE932 4.6 115.6 1.0
N D:GLY900 4.6 123.2 1.0
C D:CYS901 4.7 132.3 1.0
CA D:CYS898 4.8 140.8 1.0
CA D:PHE932 4.8 119.2 1.0
ND2 D:ASN903 4.8 151.4 1.0
N D:TYR902 4.9 131.9 1.0
CA D:CYS930 5.0 111.7 1.0

Zinc binding site 7 out of 8 in 9iic

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Zinc binding site 7 out of 8 in the Crystal Structure of Hoip RING2-Ldd in Complex with STK4 Kd 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 Hoip RING2-Ldd in Complex with STK4 Kd Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1103

b:99.0
occ:1.00
 ND1 D:HIS1001 2.1 94.3 1.0
SG D:CYS969 2.3 85.7 1.0
SG D:CYS986 2.3 116.3 1.0
SG D:CYS998 2.3 115.3 1.0
CE1 D:HIS1001 2.6 97.3 1.0
CB D:CYS986 3.2 114.1 1.0
CB D:CYS969 3.2 98.7 1.0
CG D:HIS1001 3.3 93.6 1.0
CB D:CYS998 3.4 119.7 1.0
NE2 D:HIS1001 3.8 96.9 1.0
CB D:HIS1001 4.0 97.6 1.0
N D:CYS998 4.2 114.1 1.0
CD2 D:HIS1001 4.2 92.1 1.0
CA D:CYS998 4.4 118.8 1.0
CB D:LYS988 4.4 121.8 1.0
CB D:VAL971 4.4 80.2 1.0
CG2 D:VAL971 4.4 76.5 1.0
CA D:CYS986 4.6 114.6 1.0
CA D:CYS969 4.6 109.5 1.0
N D:LYS988 4.8 124.5 1.0
N D:HIS1001 4.9 100.6 1.0
CG D:LYS988 4.9 121.3 1.0
C D:CYS986 5.0 119.8 1.0
NZ D:LYS988 5.0 114.6 1.0

Zinc binding site 8 out of 8 in 9iic

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Zinc binding site 8 out of 8 in the Crystal Structure of Hoip RING2-Ldd in Complex with STK4 Kd 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 Hoip RING2-Ldd in Complex with STK4 Kd Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1104

b:190.6
occ:1.00
 NE2 D:HIS923 2.0 207.0 1.0
NE2 D:HIS925 2.1 191.8 1.0
SG D:CYS916 2.3 201.9 1.0
SG D:CYS911 2.3 195.1 1.0
CE1 D:HIS925 2.7 193.4 1.0
CD2 D:HIS923 3.0 205.4 1.0
CE1 D:HIS923 3.1 209.4 1.0
CD2 D:HIS925 3.1 183.2 1.0
CB D:CYS911 3.4 195.4 1.0
CB D:CYS916 3.4 202.4 1.0
ND1 D:HIS925 3.8 185.7 1.0
CG D:HIS925 4.0 178.4 1.0
CG D:HIS923 4.1 208.2 1.0
ND1 D:HIS923 4.2 210.2 1.0
CA D:CYS916 4.3 203.8 1.0
CA D:CYS911 4.8 195.8 1.0
O D:VAL918 5.0 188.7 1.0

Reference:

Y.R.Wang, X.D.Zhou, L.F.Pan. Crystal Structure of Hoip RING2-Ldd in Complex with STK4 Kd Domain To Be Published.
Page generated: Fri Aug 22 18:11:27 2025

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