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Zinc in PDB 4ycg: Pro-Bone Morphogenetic Protein 9

Protein crystallography data

The structure of Pro-Bone Morphogenetic Protein 9, PDB code: 4ycg was solved by L.-Z.Mi, C.T.Brown, Y.Gao, Y.Tian, V.Le, T.Walz, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.79 / 3.30
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.780, 120.780, 220.620, 90.00, 90.00, 120.00
R / Rfree (%) 21.3 / 23

Zinc Binding Sites:

The binding sites of Zinc atom in the Pro-Bone Morphogenetic Protein 9 (pdb code 4ycg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Pro-Bone Morphogenetic Protein 9, PDB code: 4ycg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 4ycg

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Zinc binding site 1 out of 10 in the Pro-Bone Morphogenetic Protein 9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pro-Bone Morphogenetic Protein 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:0.1
occ:1.00
OE1 A:GLU212 2.1 0.8 1.0
NE2 A:HIS141 2.5 1.0 1.0
CD A:GLU212 2.5 0.7 1.0
OE2 A:GLU212 2.5 0.6 1.0
CE1 A:HIS141 2.7 0.8 1.0
CD2 A:HIS141 3.8 0.6 1.0
CG A:GLU212 3.8 0.7 1.0
ND1 A:HIS141 4.0 1.0 1.0
CA A:GLU212 4.1 0.7 1.0
CB A:GLU212 4.3 0.5 1.0
CG A:HIS141 4.6 0.5 1.0
O A:ARG211 4.7 0.1 1.0
N A:GLU212 4.9 0.8 1.0

Zinc binding site 2 out of 10 in 4ycg

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Zinc binding site 2 out of 10 in the Pro-Bone Morphogenetic Protein 9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pro-Bone Morphogenetic Protein 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:0.3
occ:1.00
OE1 A:GLU244 2.1 0.0 1.0
OE2 A:GLU120 2.1 0.4 1.0
CD A:GLU244 2.6 0.3 1.0
OE2 A:GLU244 2.6 0.1 1.0
NE2 A:HIS119 2.6 0.8 1.0
O A:HOH405 2.7 0.7 1.0
CD A:GLU120 3.1 0.4 1.0
CE1 A:HIS119 3.3 0.4 1.0
CG A:GLU120 3.4 0.8 1.0
CD2 A:HIS119 3.7 1.0 1.0
CG A:GLU244 4.0 0.5 1.0
NH2 A:ARG87 4.2 0.0 1.0
OE1 A:GLU120 4.2 0.1 1.0
CD1 A:ILE85 4.4 0.4 1.0
CA A:GLU244 4.4 0.6 1.0
ND1 A:HIS119 4.4 0.7 1.0
CB A:GLU244 4.5 0.1 1.0
CG A:PRO117 4.5 0.2 1.0
CB A:PRO117 4.7 0.6 1.0
CG A:HIS119 4.7 0.4 1.0
OD1 A:ASP237 4.8 0.3 1.0
CB A:GLU120 4.9 0.6 1.0
NZ C:LYS393 5.0 0.8 1.0
CD1 A:LEU247 5.0 0.6 1.0

Zinc binding site 3 out of 10 in 4ycg

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Zinc binding site 3 out of 10 in the Pro-Bone Morphogenetic Protein 9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pro-Bone Morphogenetic Protein 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:0.9
occ:1.00
OD1 A:ASP173 2.2 0.2 1.0
OD2 A:ASP173 2.3 0.7 1.0
CG A:ASP173 2.5 0.3 1.0
O A:HOH404 2.7 0.5 1.0
CB A:ASP173 3.9 0.9 1.0
CB A:SER146 4.8 0.7 1.0
CA A:ASP173 4.9 0.7 1.0
CE1 A:HIS210 4.9 0.5 1.0

Zinc binding site 4 out of 10 in 4ycg

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Zinc binding site 4 out of 10 in the Pro-Bone Morphogenetic Protein 9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Pro-Bone Morphogenetic Protein 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:0.8
occ:1.00
OE1 A:GLU101 2.4 0.9 1.0
O A:HOH401 3.1 0.8 1.0
O A:HOH403 3.5 0.3 1.0
CD A:GLU101 3.6 0.3 1.0
OE2 A:GLU101 4.4 0.4 1.0
CB A:GLU101 4.4 0.8 1.0
CG A:GLU101 4.6 0.4 1.0

Zinc binding site 5 out of 10 in 4ycg

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Zinc binding site 5 out of 10 in the Pro-Bone Morphogenetic Protein 9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Pro-Bone Morphogenetic Protein 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:0.7
occ:1.00
OE2 A:GLU144 2.1 0.2 1.0
ND1 A:HIS210 2.3 0.6 1.0
OE1 A:GLU144 2.7 0.7 1.0
CD A:GLU144 2.7 0.6 1.0
CE1 A:HIS210 2.9 0.5 1.0
CG A:HIS210 3.5 0.9 1.0
CB A:HIS210 4.1 0.4 1.0
NE2 A:HIS210 4.1 0.3 1.0
CG A:GLU144 4.1 0.5 1.0
CD2 A:HIS210 4.4 0.9 1.0

Zinc binding site 6 out of 10 in 4ycg

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Zinc binding site 6 out of 10 in the Pro-Bone Morphogenetic Protein 9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Pro-Bone Morphogenetic Protein 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:0.7
occ:1.00
OD2 B:ASP215 2.2 0.1 1.0
OD1 B:ASP136 2.4 1.0 1.0
OD1 B:ASP215 2.5 0.1 1.0
OD2 B:ASP136 2.5 0.9 1.0
CG B:ASP215 2.7 0.9 1.0
CG B:ASP136 2.7 0.2 1.0
CB B:ASP136 4.1 0.1 1.0
CB B:ASP215 4.2 0.2 1.0
CG2 B:THR216 4.6 0.6 1.0
O B:VAL137 4.7 0.8 1.0
O B:HOH402 4.7 98.0 1.0
N B:ASP215 4.9 0.3 1.0

Zinc binding site 7 out of 10 in 4ycg

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Zinc binding site 7 out of 10 in the Pro-Bone Morphogenetic Protein 9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Pro-Bone Morphogenetic Protein 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:0.7
occ:1.00
OD1 B:ASP173 2.1 0.6 1.0
OD2 B:ASP173 2.3 0.6 1.0
O B:HOH401 2.4 1.0 1.0
CG B:ASP173 2.5 0.9 1.0
CB B:ASP173 3.9 0.1 1.0
CB B:SER146 4.7 0.8 1.0
CE1 B:HIS210 4.7 1.0 1.0
CA B:ASP173 4.8 0.3 1.0

Zinc binding site 8 out of 10 in 4ycg

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Zinc binding site 8 out of 10 in the Pro-Bone Morphogenetic Protein 9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Pro-Bone Morphogenetic Protein 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn305

b:0.2
occ:1.00
OE1 B:GLU244 2.2 0.1 1.0
OE2 B:GLU120 2.2 0.1 1.0
OE2 B:GLU244 2.5 0.3 1.0
CD B:GLU244 2.6 0.9 1.0
NE2 B:HIS119 2.8 0.4 1.0
CD B:GLU120 3.2 0.1 1.0
CE1 B:HIS119 3.5 0.7 1.0
CG B:GLU120 3.6 0.6 1.0
CD2 B:HIS119 3.9 0.7 1.0
CG B:GLU244 4.0 0.2 1.0
NH2 B:ARG87 4.3 0.7 1.0
CA B:GLU244 4.3 0.8 1.0
OE1 B:GLU120 4.3 0.1 1.0
CB B:GLU244 4.4 0.6 1.0
CG B:PRO117 4.5 0.5 1.0
CD1 B:ILE85 4.5 0.4 1.0
ND1 B:HIS119 4.6 0.6 1.0
CB B:PRO117 4.7 0.6 1.0
O B:GLU244 4.8 0.9 1.0
OD1 B:ASP237 4.9 0.2 1.0
CG B:HIS119 4.9 1.0 1.0
NZ D:LYS393 5.0 0.8 1.0

Zinc binding site 9 out of 10 in 4ycg

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Zinc binding site 9 out of 10 in the Pro-Bone Morphogenetic Protein 9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Pro-Bone Morphogenetic Protein 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:1.0
occ:1.00
OE2 C:GLU397 2.2 0.1 1.0
CD C:GLU397 3.3 0.7 1.0
OE1 C:GLU397 3.8 0.3 1.0
CG C:HIS395 3.9 0.7 1.0
ND1 C:HIS395 4.1 0.4 1.0
CB C:HIS395 4.1 0.2 1.0
CD2 C:HIS395 4.2 0.6 1.0
CG C:PRO378 4.3 0.7 1.0
CG C:GLU397 4.5 0.4 1.0
CE1 C:HIS395 4.5 0.7 1.0
NE2 C:HIS395 4.6 0.1 1.0

Zinc binding site 10 out of 10 in 4ycg

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Zinc binding site 10 out of 10 in the Pro-Bone Morphogenetic Protein 9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Pro-Bone Morphogenetic Protein 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:0.2
occ:1.00
O C:HOH603 2.2 0.7 1.0
O C:HOH602 2.3 1.0 1.0
NE2 C:HIS359 2.4 0.4 1.0
CD2 C:HIS359 3.1 0.0 1.0
CE1 C:HIS359 3.6 0.6 1.0
CG C:HIS359 4.4 0.9 1.0
CD C:LYS368 4.4 0.5 1.0
ND1 C:HIS359 4.5 1.0 1.0
NZ C:LYS368 4.6 0.3 1.0
CE C:LYS368 4.8 0.8 1.0

Reference:

L.-Z.Mi, C.T.Brown, Y.Gao, Y.Tian, V.Le, T.Walz, T.A.Springer. Structure of Bone Morphogenetic Q:1 Protein 9 Procomplex PNAS 2015.
Page generated: Wed Dec 16 05:56:22 2020

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