Zinc in PDB 6owx: Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification

Protein crystallography data

The structure of Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification, PDB code: 6owx was solved by S.Rocchio, R.Duman, K.El Omari, V.Mykhaylyk, Z.Yan, A.Wagner, J.C.A.Bardwell, S.Horowitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.20 / 2.06
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 42.800, 42.800, 253.780, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 27.7

Other elements in 6owx:

The structure of Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification also contains other interesting chemical elements:

Iodine (I) 1 atom
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Zinc atom in the Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification (pdb code 6owx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 13 binding sites of Zinc where determined in the Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification, PDB code: 6owx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 13 in 6owx

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Zinc binding site 1 out of 13 in the Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:60.6
occ:0.65
HN1 A:IMD215 1.5 99.3 1.0
OE2 A:GLU59 2.2 94.0 1.0
N1 A:IMD215 2.3 82.9 1.0
OE1 A:GLU59 2.8 87.8 1.0
CD A:GLU59 2.8 92.2 1.0
C5 A:IMD215 3.0 91.3 1.0
H5 A:IMD215 3.0 0.3 1.0
C2 A:IMD215 3.4 0.5 1.0
H2 A:IMD215 3.7 0.6 1.0
CG A:GLU59 4.2 87.3 1.0
C4 A:IMD215 4.2 0.7 1.0
N3 A:IMD215 4.4 0.5 1.0
H A:GLU59 4.9 90.5 1.0

Zinc binding site 2 out of 13 in 6owx

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Zinc binding site 2 out of 13 in the Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:89.2
occ:0.93
H2 B:IMD201 2.3 90.8 1.0
OD2 A:ASP66 2.5 68.2 1.0
OD1 A:ASP66 2.6 52.3 1.0
C2 B:IMD201 2.9 75.9 1.0
CG A:ASP66 2.9 56.6 1.0
HN3 B:IMD201 2.9 69.4 1.0
HN3 A:IMD212 2.9 98.1 1.0
N3 B:IMD201 3.2 58.0 1.0
N3 A:IMD212 3.6 82.0 1.0
O A:ARG62 3.7 55.0 1.0
H2 A:IMD212 4.0 85.4 1.0
C2 A:IMD212 4.1 71.4 1.0
N1 B:IMD201 4.1 56.5 1.0
C A:ARG62 4.2 61.0 1.0
CB A:ARG62 4.3 61.3 1.0
CB A:ASP66 4.4 50.6 1.0
C4 B:IMD201 4.5 61.5 1.0
HA A:ARG62 4.6 68.6 1.0
C4 A:IMD212 4.6 70.3 1.0
HN1 B:IMD201 4.6 67.6 1.0
H A:ASP66 4.7 53.2 1.0
CA A:ARG62 4.7 60.2 1.0
HA A:ALA63 4.7 85.5 1.0
HB3 A:HIS65 4.8 54.5 1.0
HB2 A:ASP66 4.8 63.0 1.0
HB3 A:ASP66 4.9 63.0 1.0
H4 A:IMD212 4.9 84.1 1.0
C5 B:IMD201 4.9 74.1 1.0

Zinc binding site 3 out of 13 in 6owx

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Zinc binding site 3 out of 13 in the Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:51.3
occ:0.91
OD2 A:ASP71 2.0 50.0 1.0
O A:HOH321 2.6 0.9 1.0
CG A:ASP71 2.7 50.1 1.0
OD1 A:ASP71 2.8 48.1 1.0
O A:HOH310 4.0 64.7 1.0
O A:HOH307 4.1 58.8 1.0
CB A:ASP71 4.2 48.8 1.0
HB3 A:ASP71 4.3 69.8 1.0
HB2 A:ASP71 4.5 69.8 1.0
HG23 A:THR72 4.6 64.7 1.0
H A:ASP71 4.9 46.0 1.0

Zinc binding site 4 out of 13 in 6owx

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Zinc binding site 4 out of 13 in the Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:0.2
occ:1.00
OE2 A:GLU79 2.1 62.0 1.0
CD A:GLU79 2.9 55.8 1.0
OE1 A:GLU79 3.0 66.0 1.0
CG A:GLU79 4.3 50.7 1.0
HG3 A:GLU79 4.5 65.2 1.0
HD11 B:LEU94 4.6 62.1 1.0
HG2 A:GLU79 4.7 65.2 1.0
HZ1 B:LYS90 4.9 59.6 1.0
HZ2 B:LYS90 4.9 59.6 1.0
HD2 B:LYS90 4.9 57.1 1.0

Zinc binding site 5 out of 13 in 6owx

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Zinc binding site 5 out of 13 in the Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:57.1
occ:1.00
OE1 A:GLU86 2.0 54.5 1.0
N3 A:IMD213 2.1 65.2 1.0
CD A:GLU86 2.7 61.6 1.0
OE2 A:GLU86 2.7 63.2 1.0
C2 A:IMD213 3.1 69.1 1.0
C4 A:IMD213 3.1 66.4 1.0
H2 A:IMD213 3.2 82.7 1.0
H4 A:IMD213 3.3 79.5 1.0
CG A:GLU86 4.1 58.7 1.0
N1 A:IMD213 4.2 69.8 1.0
C5 A:IMD213 4.3 76.2 1.0
HB1 A:ALA83 4.4 65.1 1.0
O A:HOH317 4.5 50.4 1.0
CB A:GLU86 4.6 53.6 1.0

Zinc binding site 6 out of 13 in 6owx

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Zinc binding site 6 out of 13 in the Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn206

b:0.3
occ:0.95
O A:HOH304 2.2 0.5 1.0
OE2 A:GLU98 2.7 67.4 1.0
O A:HOH302 2.9 65.0 1.0
OE1 A:GLU98 3.0 62.8 1.0
CD A:GLU98 3.2 60.1 1.0
HZ1 A:LYS102 4.0 1.0 1.0
HZ2 A:LYS102 4.7 1.0 1.0
CG A:GLU98 4.7 56.8 1.0
NZ A:LYS102 4.8 67.7 1.0
HG2 A:GLU98 4.9 73.3 1.0

Zinc binding site 7 out of 13 in 6owx

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Zinc binding site 7 out of 13 in the Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn207

b:50.8
occ:1.00
HN1 B:IMD201 1.4 67.6 1.0
N1 B:IMD201 2.0 56.5 1.0
OE2 B:GLU120 2.0 52.0 1.0
ND1 A:HIS65 2.1 47.4 1.0
CL A:CL211 2.2 54.9 1.0
H5 B:IMD201 2.2 88.7 1.0
C5 B:IMD201 2.4 74.1 1.0
CD B:GLU120 2.8 56.0 1.0
OE1 B:GLU120 2.9 55.4 1.0
CE1 A:HIS65 3.0 43.1 1.0
HE1 A:HIS65 3.1 51.6 1.0
CG A:HIS65 3.2 53.9 1.0
C2 B:IMD201 3.3 75.9 1.0
HB2 A:HIS65 3.4 54.5 1.0
HD1 B:PHE119 3.5 87.1 1.0
HB3 A:HIS65 3.5 54.5 1.0
CB A:HIS65 3.6 50.2 1.0
C4 B:IMD201 3.7 61.5 1.0
HA A:ARG62 3.8 68.6 1.0
H2 B:IMD201 3.9 90.8 1.0
N3 B:IMD201 4.1 58.0 1.0
CD1 B:PHE119 4.1 59.7 1.0
NE2 A:HIS65 4.1 46.9 1.0
HA B:GLU120 4.2 75.5 1.0
CG B:GLU120 4.2 50.7 1.0
HE1 B:PHE119 4.3 82.5 1.0
CD2 A:HIS65 4.3 47.8 1.0
HG2 B:GLU120 4.4 55.4 1.0
HN1 A:IMD212 4.4 1.0 1.0
N1 A:IMD212 4.4 85.2 1.0
H4 B:IMD201 4.5 73.5 1.0
CE1 B:PHE119 4.6 59.6 1.0
HB3 B:PHE119 4.6 51.0 1.0
C5 A:IMD212 4.7 65.4 1.0
HG3 B:GLU120 4.7 55.4 1.0
CA A:ARG62 4.7 60.2 1.0
H5 A:IMD212 4.8 78.2 1.0
C2 A:IMD212 4.8 71.4 1.0
CA B:GLU120 4.9 57.3 1.0
HE2 A:HIS65 4.9 70.1 1.0

Zinc binding site 8 out of 13 in 6owx

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Zinc binding site 8 out of 13 in the Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn208

b:61.2
occ:1.00
N3 A:IMD214 2.1 81.5 1.0
OD2 A:ASP36 2.2 57.4 1.0
O A:HOH312 2.5 53.1 1.0
OD1 A:ASP36 2.7 57.5 1.0
CG A:ASP36 2.8 58.2 1.0
C2 A:IMD214 2.9 0.7 1.0
H2 A:IMD214 3.1 0.6 1.0
C4 A:IMD214 3.1 93.7 1.0
O A:HOH316 3.4 63.5 1.0
H4 A:IMD214 3.4 0.2 1.0
N1 A:IMD214 4.1 92.9 1.0
C5 A:IMD214 4.2 0.3 1.0
HZ3 A:LYS39 4.2 0.3 1.0
CB A:ASP36 4.3 50.6 1.0
HB3 A:ASP36 4.5 60.0 1.0
HB2 A:ASP36 4.6 60.0 1.0
HZ2 A:LYS39 4.7 0.3 1.0
NZ A:LYS39 4.9 62.0 1.0
HN1 A:IMD214 4.9 0.2 1.0

Zinc binding site 9 out of 13 in 6owx

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Zinc binding site 9 out of 13 in the Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn209

b:0.3
occ:0.41
OE2 A:GLU87 2.5 78.2 1.0
O A:HOH311 2.9 60.0 1.0
HZ2 A:LYS90 3.0 64.0 1.0
HZ3 A:LYS90 3.0 64.0 1.0
CD A:GLU87 3.3 75.0 1.0
NZ A:LYS90 3.4 60.3 1.0
HD3 A:LYS90 3.5 80.0 1.0
OE1 A:GLU87 3.5 76.5 1.0
O A:HOH315 3.7 45.2 1.0
HD2 A:LYS90 4.0 80.0 1.0
CD A:LYS90 4.1 62.0 1.0
HZ1 A:LYS90 4.1 64.0 1.0
CE A:LYS90 4.3 64.3 1.0
CG A:GLU87 4.5 66.7 1.0
OE2 A:GLU86 4.6 63.2 1.0
HE2 A:LYS90 4.8 85.1 1.0

Zinc binding site 10 out of 13 in 6owx

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Zinc binding site 10 out of 13 in the Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Spy H96L:IM7 L18PI-Phe Complex; Multiple Anomalous Datasets Contained Herein For Element Identification within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn216

b:56.0
occ:1.00
OE2 A:GLU120 1.6 54.0 1.0
ND1 B:HIS65 2.2 46.3 1.0
CL A:CL210 2.3 67.5 1.0
CD A:GLU120 2.7 57.7 1.0
OE1 A:GLU120 3.1 58.8 1.0
CE1 B:HIS65 3.2 49.8 1.0
CG B:HIS65 3.2 49.4 1.0
HB2 B:HIS65 3.2 68.8 1.0
HD1 A:PHE119 3.3 85.9 1.0
HE1 B:HIS65 3.3 70.4 1.0
HB3 B:HIS65 3.3 68.8 1.0
CB B:HIS65 3.4 51.6 1.0
HA B:ARG62 3.8 87.0 1.0
CG A:GLU120 4.0 58.5 1.0
HG2 A:GLU120 4.0 56.4 1.0
CD1 A:PHE119 4.1 53.7 1.0
HA A:GLU120 4.1 76.8 1.0
HE1 A:PHE119 4.3 75.8 1.0
NE2 B:HIS65 4.3 48.5 1.0
CD2 B:HIS65 4.3 47.9 1.0
HB3 A:PHE119 4.4 66.6 1.0
HG3 A:GLU120 4.5 56.4 1.0
CE1 A:PHE119 4.6 48.2 1.0
CA B:ARG62 4.8 62.1 1.0
CA A:GLU120 4.8 61.1 1.0
CB A:GLU120 4.9 59.1 1.0
CA B:HIS65 5.0 52.2 1.0

Reference:

S.Rocchio, R.Duman, K.El Omari, V.Mykhaylyk, Z.Yan, A.Wagner, J.C.A.Bardwell, S.Horowitz. Identifying Dynamic, Partially Occupied Residues Using Anomalous Scattering To Be Published.
Page generated: Wed Dec 16 12:28:11 2020

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