Calcium in PDB 8zb3: Crystal Structure of Nudc From Mycobacterium Abscessus

All present enzymatic activity of Crystal Structure of Nudc From Mycobacterium Abscessus:
3.6.1.22;

The structure of Crystal Structure of Nudc From Mycobacterium Abscessus, PDB code: 8zb3 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)	39.82 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.009, 133.549, 118.73, 90, 95.22, 90
R / Rfree (%)	19.7 / 22.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Nudc From Mycobacterium Abscessus (pdb code 8zb3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Crystal Structure of Nudc From Mycobacterium Abscessus, PDB code: 8zb3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in the Crystal Structure of Nudc From Mycobacterium Abscessus


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:46.6 occ:1.00 OD2 A:ASP20 1.9 46.0 1.0 OE1 A:GLU21 2.2 50.7 1.0 O B:ASP251 2.2 33.8 1.0 OE1 B:GLU210 2.3 66.8 1.0 CG A:ASP20 3.0 46.8 1.0 CD A:GLU21 3.3 50.2 1.0 C B:ASP251 3.3 42.2 1.0 CD B:GLU210 3.4 63.2 1.0 OD1 A:ASP20 3.5 45.0 1.0 CG A:GLU21 3.9 41.6 1.0 CB B:ASP251 3.9 58.8 1.0 CA B:ASP251 3.9 47.3 1.0 CG B:GLU210 4.3 55.9 1.0 CB A:ASP20 4.3 42.6 1.0 OE2 B:GLU210 4.3 58.6 1.0 OE2 A:GLU21 4.4 58.7 1.0 N B:GLY252 4.4 48.4 1.0 CB B:GLU210 4.5 42.8 1.0 CG B:ASP251 4.6 74.0 1.0 CA B:GLY252 4.7 46.7 1.0 OD2 B:ASP251 4.7 84.3 1.0 N A:GLU21 4.8 41.6 1.0 O B:HOH530 4.9 40.4 1.0

Calcium binding site 2 out of 16 in the Crystal Structure of Nudc From Mycobacterium Abscessus


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:78.4 occ:1.00 OE1 A:GLU211 2.6 71.3 1.0 O A:ALA191 2.6 33.5 1.0 OE2 A:GLU207 3.1 53.3 1.0 CD A:GLU211 3.2 68.2 1.0 OE2 A:GLU211 3.7 74.2 1.0 C A:ALA191 3.8 31.2 1.0 CA A:GLY192 3.9 31.4 1.0 CD A:GLU207 4.1 44.8 1.0 CG A:GLU211 4.1 59.2 1.0 N A:GLY192 4.3 31.1 1.0 OE1 A:GLU207 4.6 51.7 1.0 OD2 A:ASP251 4.8 78.8 1.0 CG A:GLU253 4.9 93.3 1.0

Calcium binding site 3 out of 16 in the Crystal Structure of Nudc From Mycobacterium Abscessus


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:51.7 occ:1.00 O A:HOH527 2.5 40.3 1.0 OD1 A:ASP107 2.6 50.5 1.0 O A:ASP51 2.6 39.5 1.0 OD2 A:ASP107 3.1 60.9 1.0 CG A:ASP107 3.2 49.8 1.0 C A:ASP51 3.8 36.0 1.0 CA A:GLY52 4.4 34.0 1.0 C A:GLY52 4.6 36.5 1.0 N A:GLY52 4.6 32.3 1.0 CB A:ASP51 4.7 35.6 1.0 CB A:ASP107 4.7 33.0 1.0 CB A:GLN53 4.7 38.4 1.0 NE2 A:GLN53 4.8 62.6 1.0 N A:GLN53 4.8 36.1 1.0 CA A:ASP51 4.9 35.3 1.0

Calcium binding site 4 out of 16 in the Crystal Structure of Nudc From Mycobacterium Abscessus


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:79.2 occ:1.00 OD2 A:ASP88 2.3 86.3 1.0 CG A:ASP88 3.5 78.3 1.0 O A:LEU89 3.7 44.1 1.0 CA A:ASP90 4.1 60.4 1.0 C A:LEU89 4.2 56.2 1.0 OD1 A:ASP88 4.2 80.3 1.0 N A:ASP90 4.4 58.4 1.0 CB A:ASP88 4.6 69.5 1.0 OD1 A:ASP90 4.7 65.5 1.0 N A:GLU91 4.8 58.7 1.0 CB A:ASP90 4.9 64.1 1.0 N A:LEU89 5.0 62.2 1.0

Calcium binding site 5 out of 16 in the Crystal Structure of Nudc From Mycobacterium Abscessus


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:54.9 occ:1.00 OE2 B:GLU21 2.4 62.0 1.0 O B:HOH538 2.4 56.1 1.0 OD1 B:ASP20 2.7 54.5 1.0 CD B:GLU21 3.3 63.6 1.0 OE1 B:GLU21 3.7 60.9 1.0 CG B:ASP20 3.9 62.3 1.0 N B:ASP20 4.3 41.8 1.0 CG B:GLU21 4.5 59.4 1.0 O B:HOH541 4.5 44.7 1.0 CG A:GLU210 4.5 55.9 1.0 CA B:ALA19 4.6 37.5 1.0 N B:GLU21 4.6 50.5 1.0 OD2 B:ASP20 4.6 66.8 1.0 CB B:GLU21 4.8 56.4 1.0 C B:ALA19 4.8 37.3 1.0 CB A:ASN250 4.9 75.3 1.0 ND2 A:ASN250 4.9 78.8 1.0 CB B:ASP20 5.0 49.0 1.0

Calcium binding site 6 out of 16 in the Crystal Structure of Nudc From Mycobacterium Abscessus


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:72.0 occ:1.00 O C:HOH551 2.4 50.2 1.0 OE2 C:GLU21 2.6 50.6 1.0 CD C:GLU21 3.4 44.1 1.0 OD2 F:ASP251 3.7 110.6 1.0 OE1 C:GLU21 3.8 37.5 1.0 CG F:GLU210 4.3 51.0 1.0 CG F:ASP251 4.5 107.1 1.0 CG C:GLU21 4.6 47.4 1.0 CB F:ASN250 4.7 80.7 1.0 N C:ASP20 4.7 38.6 1.0 CG F:ASN250 4.8 85.2 1.0 N C:GLU21 4.8 37.1 1.0 CA F:GLU210 4.8 41.2 1.0 CB C:GLU21 4.9 46.5 1.0 OD1 F:ASP251 4.9 110.1 1.0 CA C:ALA19 4.9 35.7 1.0

Calcium binding site 7 out of 16 in the Crystal Structure of Nudc From Mycobacterium Abscessus


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:69.7 occ:1.00 OE1 C:GLU195 2.6 32.7 1.0 O C:HOH543 2.7 43.0 1.0 CD C:GLU195 3.6 30.5 1.0 OE1 C:GLU207 3.7 47.3 1.0 CG C:GLU195 3.9 27.3 1.0 NH1 C:ARG206 4.1 39.0 1.0 NH1 F:ARG23 4.4 26.9 1.0 O C:PHE193 4.5 32.8 1.0 NH2 C:ARG206 4.5 37.6 1.0 CZ C:ARG206 4.6 38.1 1.0 OE2 C:GLU195 4.8 30.9 1.0 OE2 C:GLU210 4.9 55.0 1.0 CD C:GLU207 4.9 41.8 1.0

Calcium binding site 8 out of 16 in the Crystal Structure of Nudc From Mycobacterium Abscessus


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:48.4 occ:1.00 OD1 D:ASP51 2.3 36.4 1.0 CG D:ASP51 3.3 40.9 1.0 CB D:ASP51 3.9 39.6 1.0 CA D:ASP51 4.0 38.3 1.0 OD2 D:ASP51 4.3 43.0 1.0 C D:ASP51 4.9 38.4 1.0

Calcium binding site 9 out of 16 in the Crystal Structure of Nudc From Mycobacterium Abscessus


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca402 b:66.5 occ:1.00 OE2 D:GLU296 2.5 57.5 1.0 OE1 D:GLU296 2.6 52.0 1.0 CD D:GLU296 2.9 59.1 1.0 CB D:SER287 4.1 66.8 1.0 OE2 D:GLU293 4.2 48.6 1.0 CG D:GLU296 4.4 57.6 1.0 ND2 D:ASN7 4.4 73.3 1.0 NH2 D:ARG6 4.7 94.8 1.0 OG D:SER287 5.0 56.4 1.0

Calcium binding site 10 out of 16 in the Crystal Structure of Nudc From Mycobacterium Abscessus


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca403 b:69.7 occ:1.00 OD1 D:ASP58 2.3 95.4 1.0 O D:ALA34 2.4 59.7 1.0 O D:HOH535 2.9 47.7 1.0 CG D:ASP58 3.1 74.9 1.0 OD2 D:ASP58 3.3 83.7 1.0 C D:ALA34 3.5 53.1 1.0 CB D:ALA60 3.8 63.6 1.0 CA D:GLU35 4.0 54.0 1.0 N D:GLU35 4.2 47.1 1.0 OE2 D:GLU35 4.3 73.7 1.0 CB D:ASP58 4.4 62.2 1.0 C D:GLU35 4.5 54.4 1.0 N D:ALA60 4.6 57.7 1.0 CA D:ALA34 4.7 57.1 1.0 N D:ALA36 4.7 48.1 1.0 O D:ALA36 4.8 45.5 1.0 CD D:GLU35 4.8 74.2 1.0 CA D:ASP58 4.9 59.5 1.0 CA D:ALA60 4.9 67.0 1.0

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