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Calcium in PDB 8zb5: Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp

Enzymatic activity of Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp

All present enzymatic activity of Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp:
3.6.1.22;

Protein crystallography data

The structure of Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp, PDB code: 8zb5 was solved by L.Meng, Y.Zhang, J.Xu, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 2.60
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 131.999, 131.999, 174.314, 90, 90, 120
R / Rfree (%) 22 / 26.9

Calcium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp (pdb code 8zb5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp, PDB code: 8zb5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 13 in 8zb5

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Calcium binding site 1 out of 13 in the Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:104.9
occ:1.00
 O B:HOH505 2.4 80.8 1.0
O B:ALA191 2.8 68.2 1.0
OE1 B:GLU211 2.8 128.4 1.0
O1P B:AMP408 2.9 161.3 1.0
OE1 B:GLU253 3.2 164.7 1.0
O2P B:AMP408 3.4 175.4 1.0
CD B:GLU211 3.7 121.8 1.0
C B:ALA191 3.7 72.7 1.0
P B:AMP408 3.7 178.1 1.0
OE2 B:GLU211 3.8 125.7 1.0
C5' B:AMP408 4.4 152.3 1.0
CD B:GLU253 4.4 161.1 1.0
N B:GLY192 4.5 71.0 1.0
NE2 B:GLN179 4.5 134.0 1.0
CA B:ALA191 4.5 72.7 1.0
CA B:GLY192 4.6 63.7 1.0
O5' B:AMP408 4.6 173.0 1.0
N B:ALA191 4.6 69.5 1.0
CB B:ALA191 4.7 70.3 1.0
CD B:GLN179 4.8 126.8 1.0
OE1 B:GLN179 4.9 127.7 1.0
CA B:CA404 4.9 128.9 1.0
O3P B:AMP408 5.0 156.8 1.0

Calcium binding site 2 out of 13 in 8zb5

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Calcium binding site 2 out of 13 in the Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:118.4
occ:1.00
 O B:HOH501 2.2 86.3 1.0
OE1 B:GLU207 2.7 90.3 1.0
O3P B:AMP408 3.1 156.8 1.0
OE1 B:GLU195 3.3 64.6 1.0
NH1 B:ARG206 3.7 78.3 1.0
CD B:GLU207 3.9 83.9 1.0
OE2 B:GLU210 4.0 106.4 1.0
P B:AMP408 4.1 178.1 1.0
O2P B:AMP408 4.1 175.4 1.0
CA B:CA404 4.3 128.9 1.0
CD B:GLU195 4.3 61.8 1.0
OE2 B:GLU207 4.4 93.4 1.0
O5' B:AMP408 4.5 173.0 1.0
NH2 B:ARG206 4.5 81.3 1.0
CZ B:ARG206 4.5 81.1 1.0
O B:PHE193 4.6 54.0 1.0
OD1 A:ASP20 4.7 142.3 1.0
CG B:GLU195 4.7 53.5 1.0
CD B:GLU210 5.0 108.0 1.0

Calcium binding site 3 out of 13 in 8zb5

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Calcium binding site 3 out of 13 in the Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:109.8
occ:1.00
 OE1 B:GLU21 3.1 126.8 1.0
OE2 B:GLU21 3.3 111.6 1.0
OD1 B:ASP20 3.4 115.3 1.0
CD B:GLU21 3.6 123.1 1.0
CG A:GLU210 4.2 122.5 1.0
OD1 B:ASP17 4.4 115.5 1.0
CG B:ASP20 4.7 108.7 1.0
OE1 A:GLU210 4.9 156.1 1.0
CA B:ALA19 4.9 80.5 1.0
N B:ASP20 5.0 93.0 1.0
CD A:GLU210 5.0 145.1 1.0

Calcium binding site 4 out of 13 in 8zb5

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Calcium binding site 4 out of 13 in the Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:128.9
occ:1.00
 O2P B:AMP408 2.3 175.4 1.0
O B:HOH501 2.3 86.3 1.0
OD2 B:ASP251 2.5 157.9 1.0
OE2 B:GLU207 2.8 93.4 1.0
OE1 B:GLU211 2.9 128.4 1.0
OE2 B:GLU253 3.3 154.3 1.0
OE1 B:GLU253 3.4 164.7 1.0
OE2 B:GLU210 3.5 106.4 1.0
CD B:GLU253 3.5 161.1 1.0
CG B:GLU211 3.6 106.9 1.0
CD B:GLU211 3.7 121.8 1.0
CG B:ASP251 3.7 151.0 1.0
CD B:GLU207 3.7 83.9 1.0
P B:AMP408 3.8 178.1 1.0
OE1 B:GLU207 3.9 90.3 1.0
CB B:ASP251 4.3 145.3 1.0
CA B:CA402 4.3 118.4 1.0
O3P B:AMP408 4.3 156.8 1.0
O5' B:AMP408 4.3 173.0 1.0
CB B:GLU210 4.5 97.5 1.0
CD B:GLU210 4.7 108.0 1.0
CG B:GLU253 4.7 153.4 1.0
OD1 B:ASP251 4.7 139.2 1.0
O1P B:AMP408 4.8 161.3 1.0
OE2 B:GLU211 4.9 125.7 1.0
CA B:CA401 4.9 104.9 1.0
OD2 A:ASP20 5.0 128.0 1.0
CB B:GLU211 5.0 98.9 1.0

Calcium binding site 5 out of 13 in 8zb5

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Calcium binding site 5 out of 13 in the Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:117.2
occ:1.00
 OD2 B:ASP258 2.8 121.6 1.0
OD1 B:ASP258 3.4 114.4 1.0
CG B:ASP258 3.5 115.3 1.0
O B:TRP259 4.2 91.2 1.0
NH2 B:ARG281 4.6 104.9 1.0
CB B:ASP258 5.0 108.8 1.0

Calcium binding site 6 out of 13 in 8zb5

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Calcium binding site 6 out of 13 in the Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca406

b:126.0
occ:1.00
 OD2 B:ASP92 2.9 107.5 1.0
CG B:ASP92 3.2 137.9 1.0
OD1 B:ASP90 3.2 158.4 1.0
OD2 B:ASP90 3.3 132.5 1.0
OD1 B:ASP92 3.6 156.8 1.0
CG B:ASP90 3.7 138.2 1.0
CB B:ASP92 3.9 135.2 1.0

Calcium binding site 7 out of 13 in 8zb5

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Calcium binding site 7 out of 13 in the Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca407

b:105.0
occ:1.00
 O B:HOH504 3.0 69.9 1.0
O B:HOH505 3.3 80.8 1.0
CE2 B:PHE193 3.9 51.7 1.0
CZ B:PHE193 4.1 53.8 1.0
CB B:ALA191 4.1 70.3 1.0
O1P B:AMP408 4.3 161.3 1.0
CB B:ALA162 4.4 62.3 1.0
N B:GLY192 4.4 71.0 1.0
CD2 B:PHE193 4.4 51.5 1.0
CE1 B:PHE193 4.7 53.3 1.0
C B:ALA191 4.8 72.7 1.0
CA B:GLY192 4.8 63.7 1.0
C B:GLY192 4.9 61.6 1.0
SD B:MET234 5.0 71.7 1.0

Calcium binding site 8 out of 13 in 8zb5

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Calcium binding site 8 out of 13 in the Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:125.3
occ:1.00
 OE2 A:GLU207 3.0 95.4 1.0
OE1 A:GLU195 3.2 89.1 1.0
O A:PHE193 3.8 60.0 1.0
CA A:CA406 3.9 130.6 1.0
CD A:GLU195 4.0 73.4 1.0
NH1 A:ARG206 4.1 97.5 1.0
CG A:GLU195 4.1 69.7 1.0
NH2 A:ARG206 4.2 83.8 1.0
CD A:GLU207 4.2 91.9 1.0
C8 A:AMP407 4.4 147.1 1.0
N A:PHE193 4.5 58.2 1.0
C1' A:AMP407 4.5 169.9 1.0
CB A:PHE193 4.6 65.9 1.0
CZ A:ARG206 4.6 89.8 1.0
C A:PHE193 4.6 56.8 1.0
CA A:PHE193 4.8 59.2 1.0
N9 A:AMP407 4.8 163.4 1.0
O4' A:AMP407 4.9 179.9 1.0
OE1 A:GLU207 4.9 101.9 1.0

Calcium binding site 9 out of 13 in 8zb5

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Calcium binding site 9 out of 13 in the Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:122.3
occ:1.00
 OE2 A:GLU211 2.4 136.4 1.0
OE1 A:GLU207 3.0 101.9 1.0
O A:ALA191 3.1 74.0 1.0
OE2 A:GLU253 3.1 156.5 1.0
OE1 A:GLU253 3.2 139.7 1.0
CD A:GLU211 3.5 133.6 1.0
CD A:GLU253 3.5 148.2 1.0
CA A:CA406 3.8 130.6 1.0
CD A:GLU207 3.8 91.9 1.0
CA A:GLY192 4.0 62.2 1.0
C A:ALA191 4.1 66.0 1.0
OE2 A:GLU207 4.1 95.4 1.0
CG A:GLU211 4.3 115.0 1.0
OE1 A:GLU211 4.3 140.3 1.0
N A:GLY192 4.5 63.7 1.0
CG A:GLU253 4.9 134.8 1.0

Calcium binding site 10 out of 13 in 8zb5

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Calcium binding site 10 out of 13 in the Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Nudc From Mycobacterium Abscessus in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:101.1
occ:1.00
 OD1 A:ASP92 2.5 88.7 1.0
CG A:ASP92 3.6 97.6 1.0
OD2 A:ASP92 4.1 98.5 1.0
O A:GLU91 4.6 79.7 1.0
CB A:GLU91 4.7 85.4 1.0
CB A:ASP92 4.9 91.5 1.0
C A:GLU91 4.9 81.4 1.0

Reference:

L.Meng, Z.Sun, Y.Zhang, Y.Dong, X.Du, Y.Wu, Y.Yuan, Y.Sun, Y.Xu, H.Ding, J.Liu, J.Xu. Structural Studies on Mycobacterial Nudc Reveal A Class of Zinc Independent Nadh Pyrophosphatase. J.Mol.Biol. V. 436 68864 2024.
ISSN: ESSN 1089-8638
PubMed: 39521043
DOI: 10.1016/J.JMB.2024.168864
Page generated: Thu Jul 10 08:42:58 2025

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