Zinc in PDB 7zrp: 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex

Enzymatic activity of 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex

All present enzymatic activity of 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex:
2.7.11.17;

Protein crystallography data

The structure of 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex, PDB code: 7zrp was solved by N.Helassa, S.Antonyuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.24 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.283, 72.59, 78.156, 90, 90, 90
R / Rfree (%) 20.7 / 27.2

Other elements in 7zrp:

The structure of 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex also contains other interesting chemical elements:

Calcium (Ca) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex (pdb code 7zrp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex, PDB code: 7zrp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 7zrp

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Zinc binding site 1 out of 9 in the 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn208

b:84.9
occ:1.00
 OE1 A:GLU123 2.0 97.3 1.0
O A:HOH308 2.1 45.0 1.0
CD A:GLU123 3.0 87.5 1.0
OE2 A:GLU123 3.5 86.8 1.0
CG A:GLU123 4.2 81.0 1.0
O A:HOH313 4.3 56.0 1.0
HG3 A:GLU123 4.3 81.3 1.0
HG2 A:GLU123 4.5 81.3 1.0
HB3 A:GLU119 4.8 91.2 1.0
HB3 B:PHE1 4.9 85.3 1.0

Zinc binding site 2 out of 9 in 7zrp

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Zinc binding site 2 out of 9 in the 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn209

b:98.0
occ:1.00
 OE1 C:GLU54 2.0 104.5 1.0
OE1 A:GLU83 2.0 84.4 1.0
O A:HOH312 2.9 40.1 1.0
CD A:GLU83 2.9 81.6 1.0
CD C:GLU54 3.0 94.4 1.0
OE2 A:GLU83 3.2 83.9 1.0
OE2 C:GLU54 3.3 109.2 1.0
HA C:MET51 3.8 61.1 1.0
HG2 C:MET51 3.8 64.3 1.0
O D:ASN21 4.0 53.6 1.0
HB3 D:SER23 4.1 59.7 1.0
CG C:GLU54 4.3 77.0 1.0
HB2 C:GLU54 4.3 71.1 1.0
CG A:GLU83 4.3 71.0 1.0
HB3 D:ASN21 4.3 68.0 1.0
HG2 A:GLU83 4.4 70.5 1.0
HB2 D:ASN21 4.6 68.0 1.0
HG3 C:GLU54 4.6 79.0 1.0
CB C:GLU54 4.7 69.8 1.0
HB3 C:GLU54 4.7 71.2 1.0
HB2 A:GLU83 4.7 61.6 1.0
HD3 A:ARG86 4.7 72.0 1.0
CG C:MET51 4.8 66.7 1.0
CA C:MET51 4.8 60.0 1.0
HH22 A:ARG90 4.8 81.8 1.0
CB D:ASN21 4.9 66.5 1.0
HG3 A:GLU83 4.9 70.5 1.0
HG2 C:GLU54 5.0 79.0 1.0
CB D:SER23 5.0 60.2 1.0

Zinc binding site 3 out of 9 in 7zrp

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Zinc binding site 3 out of 9 in the 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn210

b:91.2
occ:1.00
 OE2 A:GLU54 2.0 99.8 1.0
OE1 C:GLU83 2.0 105.8 1.0
OE2 C:GLU83 2.0 93.7 1.0
CD C:GLU83 2.3 95.4 1.0
CD A:GLU54 2.9 120.6 1.0
OE1 A:GLU54 3.2 124.1 1.0
O C:HOH315 3.2 45.6 1.0
HH11 C:ARG86 3.4 123.4 0.0
HD2 C:ARG86 3.8 92.2 1.0
CG C:GLU83 3.8 86.3 1.0
HA A:MET51 3.9 60.4 1.0
HG2 A:MET51 4.0 67.5 1.0
NH1 C:ARG86 4.1 122.9 1.0
HB3 B:ASN20 4.1 64.3 1.0
O B:ASN20 4.1 51.5 1.0
HG2 C:GLU83 4.1 86.9 1.0
HH12 C:ARG86 4.2 123.4 0.0
HG3 C:GLU83 4.2 86.7 1.0
HB2 B:ASN20 4.3 64.3 1.0
CG A:GLU54 4.3 109.7 1.0
HG3 A:MET51 4.3 67.5 1.0
HG2 A:GLU54 4.5 106.5 1.0
HB3 A:GLU54 4.5 90.8 1.0
HB3 B:SER22 4.6 68.9 1.0
HD3 C:ARG86 4.6 92.2 1.0
HA C:GLU83 4.6 68.3 1.0
CG A:MET51 4.6 68.3 1.0
CD C:ARG86 4.6 90.9 1.0
O B:HOH103 4.6 50.3 1.0
CB B:ASN20 4.7 63.9 1.0
HB2 C:GLU83 4.7 78.4 1.0
CB C:GLU83 4.8 80.5 1.0
CA A:MET51 4.8 61.0 1.0
CB A:GLU54 4.9 89.5 1.0
HB2 C:ARG86 4.9 75.2 1.0
HB3 A:ASP50 4.9 77.6 1.0
HG3 A:GLU54 4.9 106.7 1.0
HB2 A:GLU54 5.0 90.8 1.0

Zinc binding site 4 out of 9 in 7zrp

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Zinc binding site 4 out of 9 in the 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn211

b:86.9
occ:0.50
 OD2 A:ASP122 2.0 85.9 1.0
CG A:ASP122 3.0 73.2 1.0
HB3 A:ASP118 3.3 77.8 1.0
OD1 A:ASP122 3.3 73.2 1.0
O A:ASP118 3.8 82.2 1.0
CB A:ASP118 4.3 80.0 1.0
CB A:ASP122 4.4 62.9 1.0
HB2 A:ASP122 4.4 63.2 1.0
C A:ASP118 4.5 77.4 1.0
HB2 A:ASP118 4.6 77.8 1.0
HB3 A:ASP122 4.8 63.2 1.0
CA A:ASP118 4.9 78.3 1.0

Zinc binding site 5 out of 9 in 7zrp

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Zinc binding site 5 out of 9 in the 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn212

b:64.2
occ:1.00
 OD2 C:ASP80 2.1 82.0 1.0
OD1 A:ASP78 2.1 67.7 1.0
OE2 A:GLU84 2.1 71.6 1.0
OD2 A:ASP78 2.1 51.9 1.0
OE1 A:GLU84 2.1 71.7 1.0
OD1 C:ASP80 2.2 70.4 1.0
O C:HOH308 2.2 28.5 1.0
CG A:ASP78 2.3 68.9 1.0
CG C:ASP80 2.4 69.2 1.0
CD A:GLU84 2.5 61.8 1.0
O A:HOH301 2.7 37.9 1.0
HB2 A:ASP80 3.4 69.9 1.0
HZ2 A:LYS75 3.5 97.7 1.0
HG2 B:ARG19 3.8 85.2 1.0
CB A:ASP78 3.8 71.6 1.0
CB C:ASP80 3.9 74.4 1.0
O B:HOH101 4.0 50.6 1.0
CG A:GLU84 4.0 60.4 1.0
HB3 A:ASP78 4.1 71.2 1.0
HB2 A:ASP78 4.1 71.2 1.0
HG3 A:LYS75 4.2 90.0 1.0
HB3 C:ASP80 4.2 73.0 1.0
NZ A:LYS75 4.3 98.7 1.0
HG2 A:GLU84 4.3 59.6 1.0
HZ3 A:LYS75 4.3 97.7 1.0
HG3 A:GLU84 4.3 59.7 1.0
HB2 C:ASP80 4.3 73.0 1.0
CB A:ASP80 4.4 69.5 1.0
H A:ASP80 4.4 76.0 1.0
OXT B:SER22 4.5 76.5 1.0
OD2 A:ASP80 4.5 68.1 1.0
HG3 B:ARG19 4.6 85.1 1.0
HH22 D:ARG20 4.6 93.5 1.0
HG B:SER22 4.6 66.3 0.0
CG B:ARG19 4.6 83.3 1.0
HZ1 A:LYS75 4.7 97.7 1.0
HH11 B:ARG19 4.7 107.6 0.0
O A:ASP80 4.8 78.5 1.0
O B:SER22 4.8 63.6 1.0
HA A:ASP78 4.8 73.7 1.0
HB3 A:ASP80 4.8 69.8 1.0
HB2 A:GLU84 4.9 55.7 1.0
CG A:ASP80 4.9 67.7 1.0
CA A:ASP78 4.9 72.6 1.0
C A:ASP80 4.9 73.8 1.0
C B:SER22 4.9 69.0 1.0
HA A:LYS75 5.0 93.1 1.0
CA C:ASP80 5.0 74.2 1.0
HA C:ASP80 5.0 74.6 1.0

Zinc binding site 6 out of 9 in 7zrp

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Zinc binding site 6 out of 9 in the 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn206

b:62.2
occ:1.00
 OE2 C:GLU120 2.1 60.5 1.0
OE1 C:GLU120 2.1 53.6 1.0
CD C:GLU120 2.4 48.6 1.0
O C:HOH309 2.6 50.2 1.0
HD1 D:PHE2 3.8 61.4 1.0
O C:HOH311 3.9 66.5 1.0
CG C:GLU120 4.0 46.7 1.0
HG22 C:THR117 4.1 53.6 1.0
HG2 C:GLU120 4.3 47.9 1.0
HG3 C:GLU120 4.3 47.8 1.0
HB2 D:PHE2 4.3 63.9 1.0
CD1 D:PHE2 4.4 62.5 1.0
H C:THR117 4.8 65.0 1.0
HG1 C:THR117 4.8 52.5 0.0
HE1 D:PHE2 4.9 60.4 1.0
CE1 D:PHE2 5.0 58.9 1.0

Zinc binding site 7 out of 9 in 7zrp

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Zinc binding site 7 out of 9 in the 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn207

b:79.7
occ:1.00
 OD1 C:ASP50 2.1 75.2 1.0
CG C:ASP50 3.2 77.8 1.0
HD21 C:ASN53 3.5 67.3 0.0
OD2 C:ASP50 3.8 76.6 1.0
HA C:ASP50 4.0 73.7 1.0
ND2 C:ASN53 4.2 66.8 1.0
HD22 C:ASN53 4.3 67.3 0.0
CB C:ASP50 4.4 77.2 1.0
CA C:ASP50 4.6 73.8 1.0
HB3 C:ASP50 4.7 76.5 1.0

Zinc binding site 8 out of 9 in 7zrp

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Zinc binding site 8 out of 9 in the 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn208

b:76.2
occ:1.00
 HZ1 D:LYS7 1.7 62.9 0.0
HZ2 D:LYS7 1.8 62.9 0.0
OE2 C:GLU14 2.0 62.9 1.0
OE2 C:GLU114 2.0 83.3 1.0
NZ D:LYS7 2.1 62.7 1.0
HZ3 D:LYS7 2.6 62.9 0.0
CD C:GLU14 2.9 63.4 1.0
HD3 D:LYS7 3.0 57.1 1.0
CD C:GLU114 3.1 77.3 1.0
OE1 C:GLU14 3.2 60.1 1.0
CE D:LYS7 3.3 56.5 1.0
CD D:LYS7 3.5 56.6 1.0
HD21 C:LEU18 3.5 41.5 1.0
HD2 D:LYS7 3.6 57.0 1.0
HG2 C:GLU114 3.6 76.4 1.0
HG C:SER17 3.6 58.9 0.0
CG C:GLU114 3.8 77.2 1.0
HE2 D:LYS7 3.8 57.9 1.0
HE3 D:LYS7 3.9 57.9 1.0
HG C:LEU18 3.9 43.2 1.0
OE1 C:GLU114 4.0 76.3 1.0
HG3 C:GLU114 4.0 76.4 1.0
HD23 C:LEU18 4.1 41.5 1.0
OG C:SER17 4.2 59.5 1.0
CD2 C:LEU18 4.2 40.5 1.0
CG C:GLU14 4.3 63.7 1.0
HG3 C:GLU14 4.4 62.8 1.0
CG C:LEU18 4.6 43.7 1.0
HG2 C:GLU14 4.6 62.8 1.0
HD11 C:LEU18 4.7 42.7 1.0
HA D:LYS7 4.8 56.0 1.0
CG D:LYS7 4.9 58.4 1.0
HA C:GLU14 5.0 59.5 1.0
O C:GLU14 5.0 58.3 1.0

Zinc binding site 9 out of 9 in 7zrp

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Zinc binding site 9 out of 9 in the 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of 2.65 Angstrom Crystal Structure of Ca/Cam:Camkiidelta Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn209

b:58.9
occ:1.00
 OE2 C:GLU84 2.0 53.1 1.0
OD2 A:ASP80 2.0 68.1 1.0
OD2 C:ASP78 2.1 72.7 1.0
OD1 A:ASP80 2.1 63.3 1.0
OD1 C:ASP78 2.1 74.0 1.0
O D:HOH101 2.2 36.6 1.0
CG A:ASP80 2.3 67.7 1.0
CG C:ASP78 2.4 72.1 1.0
CD C:GLU84 2.8 58.0 1.0
OE1 C:GLU84 3.1 64.7 1.0
HB2 C:ASP80 3.4 73.0 1.0
HZ2 C:LYS75 3.4 91.1 1.0
CB A:ASP80 3.8 69.5 1.0
CB C:ASP78 3.8 72.8 1.0
HB3 A:ASP80 4.0 69.8 1.0
HE D:ARG20 4.0 84.0 1.0
HZ3 C:LYS75 4.0 91.1 1.0
NZ C:LYS75 4.1 91.2 1.0
HB3 C:ASP78 4.1 72.3 1.0
HB2 C:ASP78 4.2 72.3 1.0
HG3 D:ARG20 4.2 72.7 1.0
HB2 A:ASP80 4.2 69.9 1.0
CG C:GLU84 4.2 54.6 1.0
CB C:ASP80 4.4 74.4 1.0
OXT D:SER23 4.4 75.2 1.0
HG3 C:LYS75 4.4 84.8 1.0
HG3 C:GLU84 4.4 55.3 1.0
H C:ASP80 4.4 74.0 1.0
HZ1 C:LYS75 4.5 91.1 1.0
HG2 C:GLU84 4.5 55.3 1.0
OD2 C:ASP80 4.6 82.0 1.0
NE D:ARG20 4.7 82.7 1.0
HB3 C:ASP80 4.8 73.0 1.0
HG D:SER23 4.8 57.4 0.0
O C:HOH307 4.8 45.5 1.0
O D:SER23 4.8 58.9 1.0
HA C:ASP78 4.9 72.3 1.0
CA A:ASP80 4.9 72.7 1.0
HA A:ASP80 4.9 73.2 1.0
O C:ASP80 4.9 64.4 1.0
CG C:ASP80 4.9 69.2 1.0
C D:SER23 4.9 67.1 1.0
CA C:ASP78 5.0 71.3 1.0

Reference:

O.Prakash, N.Gupta, A.Milburn, L.Mccormick, V.Deugi, P.Fisch, J.Wyles, N.L.Thomas, S.Antonyuk, C.Dart, N.Helassa. Calmodulin Variant E140G Associated with Long Qt Syndrome Impairs Camkii Delta Autophosphorylation and L-Type Calcium Channel (Ca V 1.2) Inactivation. J.Biol.Chem. 02777 2022.
ISSN: ESSN 1083-351X
PubMed: 36496072
DOI: 10.1016/J.JBC.2022.102777
Page generated: Sat Apr 8 07:13:21 2023

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